// $Id: TreePanel.java,v 1.178 2010/10/09 03:07:29 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.archaeopteryx;
/**
* NOTE - The original file was obtained from SourceForge.net (Archaeopteryx Version 0.957 beta) on 2010.10.13
* and was modified by the LANL Influenza Sequence Database IT team (flu@lanl.gov)
*/
import gov.lanl.application.TPTD.applet.AppletParams;
import gov.lanl.application.TPTD.applet.NewWindowSubtree;
import gov.lanl.application.TPTD.applet.SubTreePanel;
import gov.lanl.application.TPTD.custom.data.Accession;
import gov.lanl.application.treeDecorator.applet.TreeDecoratorPaint;
import gov.lanl.application.treeDecorator.applet.ui.drawDecoration.DecoratorColorSet;
import gov.lanl.application.treePruner.applet.TreePrunerColorSet;
import gov.lanl.application.treePruner.applet.TreePrunerPaint;
import gov.lanl.application.treePruner.custom.data.WorkingSet;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GradientPaint;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Point;
import java.awt.Polygon;
import java.awt.Rectangle;
import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
import java.awt.event.InputEvent;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.font.FontRenderContext;
import java.awt.font.TextLayout;
import java.awt.geom.AffineTransform;
import java.awt.geom.Arc2D;
import java.awt.geom.CubicCurve2D;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Line2D;
import java.awt.geom.QuadCurve2D;
import java.awt.geom.Rectangle2D;
import java.awt.print.PageFormat;
import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.io.File;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URLEncoder;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.swing.BorderFactory;
import javax.swing.JApplet;
import javax.swing.JColorChooser;
import javax.swing.JDialog;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JTextArea;
import javax.swing.Popup;
import javax.swing.PopupFactory;
import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.PhylogenyData;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.SequenceRelation;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
//******************************************START**********************************************************//
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
private static final float PI = ( float ) ( Math.PI );
private static final double TWO_PI = 2 * Math.PI;
private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
private static final short OV_BORDER = 10;
final static Cursor CUT_CURSOR = Cursor
.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
final static Cursor MOVE_CURSOR = Cursor
.getPredefinedCursor( Cursor.MOVE_CURSOR );
final static Cursor ARROW_CURSOR = Cursor
.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
final static Cursor HAND_CURSOR = Cursor
.getPredefinedCursor( Cursor.HAND_CURSOR );
final static Cursor WAIT_CURSOR = Cursor
.getPredefinedCursor( Cursor.WAIT_CURSOR );
private final static long serialVersionUID = -978349745916505029L;
private final static int EURO_D = 10;
private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
private final static int MIN_ROOT_LENGTH = 3;
private final static int BOX_SIZE = 4;
private final static int HALF_BOX_SIZE = TreePanel.BOX_SIZE / 2;
private final static int MAX_SUBTREES = 100;
private final static int MAX_NODE_FRAMES = 10;
private final static int MOVE = 20;
private final static NumberFormat FORMATTER_CONFIDENCE;
private final static NumberFormat FORMATTER_BRANCH_LENGTH;
private final static int WIGGLE = 2;
private final static int HALF_BOX_SIZE_PLUS_WIGGLE = HALF_BOX_SIZE + WIGGLE;
private final static int LIMIT_FOR_HQ_RENDERING = 1000;
// TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
// being static anymore (02/20/2009).
private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
RenderingHints.VALUE_RENDER_DEFAULT );
private File _treefile = null;
private Configuration _configuration = null;
private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
private int _node_frame_index = 0;
private Phylogeny _phylogeny = null;
private final Phylogeny[] _phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
// private int _subtree_index = 0;
//******************************************START CHANGED**********************************************************//
private static int _subtree_index = 0;
//changed from instance variable to static variable
//********************************************END**********************************************************//
private MainPanel _main_panel = null;
private Set<PhylogenyNode> _found_nodes = null;
private PhylogenyNode _highlight_node = null;
private JPopupMenu _node_popup_menu = null;
private JMenuItem _node_popup_menu_items[] = null;
private int _longest_ext_node_info = 0;
private float _x_correction_factor = 0.0f;
private float _ov_x_correction_factor = 0.0f;
private float _x_distance = 0.0f;
private float _y_distance = 0.0f;
private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
private float _last_drag_point_x = 0;
private float _last_drag_point_y = 0;
private ControlPanel _control_panel = null;
private int _external_node_index = 0;
private final Polygon _polygon = new Polygon();
private final StringBuilder _sb = new StringBuilder();
private JColorChooser _color_chooser = null;
private double _scale_distance = 0.0;
private String _scale_label = null;
private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
private final Line2D _line = new Line2D.Float();
private final Ellipse2D _ellipse = new Ellipse2D.Float();
private final Rectangle2D _rectangle = new Rectangle2D.Float();
private Options _options = null;
private float _ov_max_width = 0;
private float _ov_max_height = 0;
private int _ov_x_position = 0;
private int _ov_y_position = 0;
private int _ov_y_start = 0;
private float _ov_y_distance = 0;
private float _ov_x_distance = 0;
private boolean _ov_on = false;
private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
private float _urt_factor = 1;
private float _urt_factor_ov = 1;
private final boolean _phy_has_branch_lengths;
private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
private boolean _in_ov_rect = false;
private boolean _in_ov = false;
private final Rectangle _ov_virtual_rectangle = new Rectangle();
final private static double _180_OVER_PI = 180.0 / Math.PI;
private static final float ROUNDED_D = 8;
private int _circ_max_depth;
private int _circ_num_ext_nodes;
private PhylogenyNode _root;
final private Arc2D _arc = new Arc2D.Double();
final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
private AffineTransform _at;
//******************************************START**********************************************************//
public SubTreePanel subTreePanel;
public TreePrunerPaint treePrunerPaint;
public TreeDecoratorPaint treeDecoratorPaint;
public WorkingSet workingSet;
public NewWindowSubtree newWindowSubtree = new NewWindowSubtree(this);
//********************************************END**********************************************************//
private double _max_distance_to_root = -1;
private int _dynamic_hiding_factor = 0;
private boolean _edited = false;
private Popup _node_desc_popup;
private JTextArea _rollover_popup;
//private final short _skip_counter = 0;
private final StringBuffer _popup_buffer = new StringBuffer();
//******************************************START**********************************************************//
final private static Font POPUP_FONT_NEW = new Font( Configuration
.getDefaultFontFamilyName(),
Font.PLAIN,
9 );
//********************************************END**********************************************************//
final private static Font POPUP_FONT = new Font( Configuration
.getDefaultFontFamilyName(),
Font.PLAIN,
12 );
private static final boolean DRAW_MEAN_COUNTS = true; //TODO remove me later
private Sequence _query_sequence = null;
private final FontRenderContext _frc = new FontRenderContext( null,
false,
false );
// private Image offscreenImage;
// private Graphics offscreenGraphics;
// private Dimension offscreenDimension;
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
}
TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
requestFocusInWindow();
addKeyListener( new KeyAdapter() {
@Override
public void keyPressed( final KeyEvent key_event ) {
keyPressedCalls( key_event );
requestFocusInWindow();
}
} );
addFocusListener( new FocusAdapter() {
@Override
public void focusGained( final FocusEvent e ) {
requestFocusInWindow();
}
} );
if ( ( t == null ) || t.isEmpty() ) {
throw new IllegalArgumentException( "ill advised attempt to draw phylogeny which is null or empty" );
}
_graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
_main_panel = tjp;
_configuration = configuration;
_phylogeny = t;
_phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
init();
if ( !_phylogeny.isEmpty() ) {
_phylogeny.recalculateNumberOfExternalDescendants( true );
}
//******************************************START**********************************************************//
if(AppletParams.isEitherTPorTDForAll()){
subTreePanel = new SubTreePanel(this);
subTreePanel.setPhylogeny(t);
subTreePanel.setSubTreeNodeInfo();
subTreePanel.setFullTreeNodeInfo();
workingSet = new WorkingSet();
treePrunerPaint = new TreePrunerPaint(this,workingSet);
treeDecoratorPaint = new TreeDecoratorPaint(this);
}
//********************************************END**********************************************************//
setBackground( getTreeColorSet().getBackgroundColor() );
final MouseListener mouse_listener = new MouseListener( this );
addMouseListener( mouse_listener );
addMouseMotionListener( mouse_listener );
addMouseWheelListener( this );
calculateScaleDistance();
FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
.getNumberOfDigitsAfterCommaForBranchLengthValues() );
}
final public void actionPerformed( final ActionEvent e ) {
int index;
boolean done = false;
final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
for( index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
// NOTE: index corresponds to the indices of click-to options
// in the control panel.
if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
// Set this as the new default click-to action
_main_panel.getControlPanel().setClickToAction( index );
final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
.getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
done = true;
}
}
repaint();
requestFocusInWindow();
}
final private void addEmptyNode( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
final String label = getASimpleTextRepresentationOfANode( node );
String msg = "";
if ( ForesterUtil.isEmpty( label ) ) {
msg = "How to add the new, empty node?";
}
else {
msg = "How to add the new, empty node to node" + label + "?";
}
final Object[] options = { "As sibling", "As descendant", "Cancel" };
final int r = JOptionPane.showOptionDialog( this,
msg,
"Addition of Empty New Node",
JOptionPane.CLOSED_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
options,
options[ 2 ] );
boolean add_as_sibling = true;
if ( r == 1 ) {
add_as_sibling = false;
}
else if ( r != 0 ) {
return;
}
final Phylogeny phy = new Phylogeny();
phy.setRoot( new PhylogenyNode() );
phy.setRooted( true );
if ( add_as_sibling ) {
if ( node.isRoot() ) {
JOptionPane.showMessageDialog( this,
"Cannot add sibling to root",
"Attempt to add sibling to root",
JOptionPane.ERROR_MESSAGE );
return;
}
phy.addAsSibling( node );
}
else {
phy.addAsChild( node );
}
_phylogeny.externalNodesHaveChanged();
_phylogeny.hashIDs();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
repaint();
}
final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
final boolean is_vertical,
final Graphics g,
final boolean to_pdf,
final boolean to_graphics_file ) {
final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
|| ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
&& ( getCutOrCopiedTree() != null )
&& ( getCopiedAndPastedNodes() != null )
&& !to_pdf
&& !to_graphics_file && getCopiedAndPastedNodes().contains( node ) ) {
g.setColor( getTreeColorSet().getFoundColor() );
}
else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
else if ( to_pdf ) {
//g.setColor( getTreeColorSet().getBranchColorForPdf() );
//******************************************START CHANGED**********************************************************//
if(AppletParams.isTreePrunerForAll() ){
treePrunerPaint.initArrayLists();
treePrunerPaint.paintKeepRemove(g,node);
}
else if(AppletParams.isTreeDecoratorForAll() ){
treeDecoratorPaint.decorateBranch(g, node);
}
else{
g.setColor( getTreeColorSet().getBranchColorForPdf() );
}
//commented - changed
//********************************************END**********************************************************//
}
else {
//g.setColor( getTreeColorSet().getBranchColor() );
//******************************************START CHANGED**********************************************************//
if(AppletParams.isTreePrunerForAll() ){
treePrunerPaint.initArrayLists();
treePrunerPaint.paintKeepRemove(g,node);
}
else if(AppletParams.isTreeDecoratorForAll() ){
treeDecoratorPaint.decorateBranch(g, node);
}
else{
g.setColor( getTreeColorSet().getBranchColor() );
}
//commented - changed
//********************************************END**********************************************************//
}
}
final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) {
if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
//******************************************START CHANGED**********************************************************//
if(AppletParams.isTreePrunerForAll() ){
treePrunerPaint.initArrayLists();
treePrunerPaint.paintKeepRemove(g,node);
_control_panel.controlPanelAdditions.callTreePrunerAutoSaveToRefresh();
}
else{
g.setColor( getTreeColorSet().getBranchColor() );
}
//changed
//********************************************END**********************************************************//
//g.setColor( getTreeColorSet().getBranchColor() );
}
}
final private void blast( final PhylogenyNode node ) {
if ( !isCanBlast( node ) ) {
JOptionPane.showMessageDialog( this,
"No sequence information present",
"Cannot Blast",
JOptionPane.WARNING_MESSAGE );
return;
}
if ( node.getNodeData().isHasSequence() ) {
String name = "";
if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
name = node.getNodeData().getSequence().getName();
}
else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
name = node.getNodeData().getSequence().getSymbol();
}
else if ( node.getNodeData().getSequence().getAccession() != null ) {
name = node.getNodeData().getSequence().getAccession().getValue();
}
if ( !ForesterUtil.isEmpty( name ) ) {
try {
System.out.println( "trying: " + name );
final Blast s = new Blast();
s.go( name );
}
catch ( final Exception e ) {
e.printStackTrace();
}
}
}
}
final void calcMaxDepth() {
if ( _phylogeny != null ) {
_circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
}
}
/**
* Calculate the length of the distance between the given node and its
* parent.
*
* @param node
* @param ext_node_x
* @factor
* @return the distance value
*/
final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
if ( getControlPanel().isDrawPhylogram() ) {
if ( node.getDistanceToParent() < 0.0 ) {
return 0.0f;
}
return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
}
else {
if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
return getXdistance();
}
return getXdistance() * factor;
}
}
final private Color calculateColorForAnnotation( final PhylogenyData ann ) {
Color c = getTreeColorSet().getAnnotationColor();
if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() );
if ( c == null ) {
c = getTreeColorSet().getAnnotationColor();
}
}
return c;
}
final void calculateLongestExtNodeInfo() {
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
int longest = 20;
for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
int sum = 0;
if ( node.isCollapse() ) {
continue;
}
if ( getControlPanel().isShowNodeNames() ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeName() + " " );
}
if ( node.getNodeData().isHasSequence() ) {
if ( getControlPanel().isShowSequenceAcc()
&& ( node.getNodeData().getSequence().getAccession() != null ) ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
.getValue()
+ " " );
}
if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
}
if ( getControlPanel().isShowGeneSymbols()
&& ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
}
if ( getControlPanel().isShowAnnotation()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotations()
.get( 0 ).asSimpleText()
+ " " );
}
}
if ( node.getNodeData().isHasTaxonomy() ) {
final Taxonomy tax = node.getNodeData().getTaxonomy();
if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
}
if ( getControlPanel().isShowTaxonomyScientificNames()
&& !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
}
if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
}
}
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString() );
}
if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
.getRenderingSize().getWidth();
}
if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
return;
}
if ( sum > longest ) {
longest = sum;
}
}
if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
}
else {
setLongestExtNodeInfo( longest );
}
}
final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
if ( getControlPanel().isDrawPhylogram() ) {
if ( node.getDistanceToParent() < 0.0 ) {
return 0.0f;
}
return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
}
else {
if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
return getOvXDistance();
}
return getOvXDistance() * factor;
}
}
final void calculateScaleDistance() {
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
final double height = getMaxDistanceToRoot();
if ( height > 0 ) {
if ( ( height <= 0.5 ) ) {
setScaleDistance( 0.01 );
}
else if ( height <= 5.0 ) {
setScaleDistance( 0.1 );
}
else if ( height <= 50.0 ) {
setScaleDistance( 1 );
}
else if ( height <= 500.0 ) {
setScaleDistance( 10 );
}
else {
setScaleDistance( 100 );
}
}
else {
setScaleDistance( 0.0 );
}
String scale_label = String.valueOf( getScaleDistance() );
if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
}
setScaleLabel( scale_label );
}
final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
String species = tax.getTaxonomyCode();
if ( ForesterUtil.isEmpty( species ) ) {
species = tax.getScientificName();
if ( ForesterUtil.isEmpty( species ) ) {
species = tax.getCommonName();
}
}
if ( ForesterUtil.isEmpty( species ) ) {
return getTreeColorSet().getTaxonomyColor();
}
// Look in species hash
Color c = getControlPanel().getSpeciesColors().get( species );
if ( c == null ) {
c = Util.calculateColorFromString( species );
getControlPanel().getSpeciesColors().put( species, c );
}
return c;
}
final private void cannotOpenBrowserWarningMessage( final String type_type ) {
JOptionPane.showMessageDialog( this,
"Cannot launch web browser for " + type_type + " data of this node",
"Cannot launch web browser",
JOptionPane.WARNING_MESSAGE );
}
/**
* Collapse the tree from the given node
*
* @param node
* a PhylogenyNode
*/
final void collapse( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
JOptionPane.showMessageDialog( this,
"Cannot collapse in unrooted display type",
"Attempt to collapse in unrooted display",
JOptionPane.WARNING_MESSAGE );
return;
}
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
Util.collapseSubtree( node, collapse );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
resetPreferredSize();
updateOvSizes();
_main_panel.adjustJScrollPane();
repaint();
}
}
final void collapseSpeciesSpecificSubtrees() {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
}
setWaitCursor();
Util.collapseSpeciesSpecificSubtrees( _phylogeny );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
resetPreferredSize();
_main_panel.adjustJScrollPane();
setArrowCursor();
repaint();
}
final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
JOptionPane.showMessageDialog( this,
"Cannot colorize subtree in unrooted display type",
"Attempt to colorize subtree in unrooted display",
JOptionPane.WARNING_MESSAGE );
return;
}
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
it.next().getBranchData().setBranchColor( new BranchColor( c ) );
}
repaint();
}
final private void colorSubtree( final PhylogenyNode node ) {
Color intitial_color = null;
if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
&& ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
intitial_color = PhylogenyMethods.getBranchColorValue( node );
}
else {
intitial_color = getTreeColorSet().getBranchColor();
}
_color_chooser.setColor( intitial_color );
_color_chooser.setPreviewPanel( new JPanel() );
final JDialog dialog = JColorChooser
.createDialog( this,
"Subtree colorization",
true,
_color_chooser,
new SubtreeColorizationActionListener( _color_chooser, node ),
null );
dialog.setVisible( true );
}
final void confColor() {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
}
setWaitCursor();
Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
setArrowCursor();
repaint();
}
final private void copySubtree( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
setCutOrCopiedTree( _phylogeny.subTree( node ) );
final Set<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
nodes.add( node );
setCopiedAndPastedNodes( nodes );
repaint();
}
final private void cutSubtree( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
if ( node.isRoot() ) {
JOptionPane.showMessageDialog( this,
"Cannot cut entire tree as subtree",
"Attempt to cut entire tree",
JOptionPane.ERROR_MESSAGE );
return;
}
final String label = getASimpleTextRepresentationOfANode( node );
final int r = JOptionPane.showConfirmDialog( null,
"Cut subtree" + label + "?",
"Confirm Cutting of Subtree",
JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.OK_OPTION ) {
return;
}
setCopiedAndPastedNodes( null );
setCutOrCopiedTree( _phylogeny.subTree( node ) );
_phylogeny.deleteSubtree( node, true );
_phylogeny.hashIDs();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
repaint();
}
final private void cycleColors() {
getMainPanel().getTreeColorSet().cycleColorScheme();
for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
}
}
final void decreaseDomainStructureEvalueThreshold() {
if ( _domain_structure_e_value_thr_exp > -20 ) {
_domain_structure_e_value_thr_exp -= 1;
}
}
final private void decreaseOvSize() {
if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
setOvMaxWidth( getOvMaxWidth() - 5 );
setOvMaxHeight( getOvMaxHeight() - 5 );
updateOvSettings();
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
if ( node.isRoot() ) {
JOptionPane.showMessageDialog( this,
"Cannot delete entire tree",
"Attempt to delete entire tree",
JOptionPane.ERROR_MESSAGE );
return;
}
final String label = getASimpleTextRepresentationOfANode( node );
final Object[] options = { "Node only", "Entire subtree", "Cancel" };
final int r = JOptionPane.showOptionDialog( this,
"Delete" + label + "?",
"Delete Node/Subtree",
JOptionPane.CLOSED_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
options,
options[ 2 ] );
boolean node_only = true;
if ( r == 1 ) {
node_only = false;
}
else if ( r != 0 ) {
return;
}
if ( node_only ) {
PhylogenyMethods.removeNode( node, _phylogeny );
}
else {
_phylogeny.deleteSubtree( node, true );
}
_phylogeny.externalNodesHaveChanged();
_phylogeny.hashIDs();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
repaint();
}
final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
makePopupMenus( node );
_node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
_node_popup_menu.show( this, x, y );
}
final private void drawArc( final double x,
final double y,
final double width,
final double heigth,
final double start_angle,
final double arc_angle,
final Graphics2D g ) {
_arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
g.draw( _arc );
}
final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
return;
}
_line.setLine( x1, y1, x2, y2 );
g.draw( _line );
}
final private void drawOval( final double x,
final double y,
final double width,
final double heigth,
final Graphics2D g ) {
_ellipse.setFrame( x, y, width, heigth );
g.draw( _ellipse );
}
final private void drawOvalFilled( final double x,
final double y,
final double width,
final double heigth,
final Graphics2D g ) {
_ellipse.setFrame( x, y, width, heigth );
g.fill( _ellipse );
}
final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
_rectangle.setFrame( x, y, width, heigth );
g.draw( _rectangle );
}
final private void drawRectFilled( final double x,
final double y,
final double width,
final double heigth,
final Graphics2D g ) {
_rectangle.setFrame( x, y, width, heigth );
g.fill( _rectangle );
}
final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
JOptionPane.showMessageDialog( this,
"Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
"Attempt to cut/copy/paste/add/delete in unrooted display",
JOptionPane.ERROR_MESSAGE );
}
/**
* Find the node, if any, at the given location
*
* @param x
* @param y
* @return pointer to the node at x,y, null if not found
*/
final PhylogenyNode findNode( final int x, final int y ) {
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return null;
}
for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
&& ( ( node.getXcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= x )
&& ( ( node.getXcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= x )
&& ( ( node.getYcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= y )
&& ( ( node.getYcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= y ) ) {
return node;
}
}
return null;
}
final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
final String tax = PhylogenyMethods.getSpecies( node );
String label = node.getNodeName();
if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
label = label + " " + tax;
}
else if ( !ForesterUtil.isEmpty( tax ) ) {
label = tax;
}
else {
label = "";
}
if ( !ForesterUtil.isEmpty( label ) ) {
label = " [" + label + "]";
}
return label;
}
final Configuration getConfiguration() {
return _configuration;
}
final ControlPanel getControlPanel() {
return _control_panel;
}
final private Set<PhylogenyNode> getCopiedAndPastedNodes() {
return getMainPanel().getCopiedAndPastedNodes();
}
final private Phylogeny getCutOrCopiedTree() {
return getMainPanel().getCutOrCopiedTree();
}
final int getDomainStructureEvalueThreshold() {
return _domain_structure_e_value_thr_exp;
}
final Set<PhylogenyNode> getFoundNodes() {
return _found_nodes;
}
final private float getLastDragPointX() {
return _last_drag_point_x;
}
final private float getLastDragPointY() {
return _last_drag_point_y;
}
final int getLongestExtNodeInfo() {
return _longest_ext_node_info;
}
final public MainPanel getMainPanel() {
return _main_panel;
}
final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
if ( !_nodeid_dist_to_leaf.containsKey( node.getNodeId() ) ) {
final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
_nodeid_dist_to_leaf.put( node.getNodeId(), m );
return m;
}
else {
return _nodeid_dist_to_leaf.get( node.getNodeId() );
}
}
final private double getMaxDistanceToRoot() {
if ( _max_distance_to_root < 0 ) {
recalculateMaxDistanceToRoot();
}
return _max_distance_to_root;
}
final Options getOptions() {
if ( _options == null ) {
_options = getControlPanel().getOptions();
}
return _options;
}
final private float getOvMaxHeight() {
return _ov_max_height;
}
final private float getOvMaxWidth() {
return _ov_max_width;
}
final Rectangle2D getOvRectangle() {
return _ov_rectangle;
}
final Rectangle getOvVirtualRectangle() {
return _ov_virtual_rectangle;
}
final private float getOvXcorrectionFactor() {
return _ov_x_correction_factor;
}
final private float getOvXDistance() {
return _ov_x_distance;
}
final private int getOvXPosition() {
return _ov_x_position;
}
final private float getOvYDistance() {
return _ov_y_distance;
}
final private int getOvYPosition() {
return _ov_y_position;
}
final private int getOvYStart() {
return _ov_y_start;
}
/**
* Get a pointer to the phylogeny
*
* @return a pointer to the phylogeny
*/
final Phylogeny getPhylogeny() {
return _phylogeny;
}
final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
return _graphics_type;
}
final private double getScaleDistance() {
return _scale_distance;
}
final private String getScaleLabel() {
return _scale_label;
}
final double getStartingAngle() {
return _urt_starting_angle;
}
/**
* Find a color for this species name.
*
* @param species
* @return the species color
*/
final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy() ) {
return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
}
// return non-colorized color
return getTreeColorSet().getTaxonomyColor();
}
/**
* @return pointer to colorset for tree drawing
*/
final TreeColorSet getTreeColorSet() {
return getMainPanel().getTreeColorSet();
}
final File getTreeFile() {
return _treefile;
}
final private TreeFontSet getTreeFontSet() {
return getMainPanel().getTreeFontSet();
}
final private float getUrtFactor() {
return _urt_factor;
}
final private float getUrtFactorOv() {
return _urt_factor_ov;
}
final float getXcorrectionFactor() {
return _x_correction_factor;
}
final float getXdistance() {
return _x_distance;
}
final float getYdistance() {
return _y_distance;
}
final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
switch ( action ) {
case SHOW_DATA:
showNodeFrame( node );
break;
case COLLAPSE:
collapse( node );
break;
case REROOT:
reRoot( node );
break;
case SUBTREE:
subTree( node );
break;
case SWAP:
swap( node );
break;
case COLOR_SUBTREE:
colorSubtree( node );
break;
case OPEN_SEQ_WEB:
openSeqWeb( node );
break;
case BLAST:
blast( node );
break;
case OPEN_TAX_WEB:
openTaxWeb( node );
break;
//******************************************START**********************************************************//
case KEEP_SEQUENCES:
workingSet.memorizeKeepNodes(node, this);
break;
case REMOVE_SEQUENCES:
workingSet.memorizeRemoveNodes(node);
break;
//********************************************END**********************************************************//
case CUT_SUBTREE:
cutSubtree( node );
break;
case COPY_SUBTREE:
copySubtree( node );
break;
case PASTE_SUBTREE:
pasteSubtree( node );
break;
case DELETE_NODE_OR_SUBTREE:
deleteNodeOrSubtree( node );
break;
case ADD_NEW_NODE:
addEmptyNode( node );
break;
case EDIT_NODE_DATA:
showNodeEditFrame( node );
break;
default:
throw new IllegalArgumentException( "unknown action: " + action );
}
}
final void increaseDomainStructureEvalueThreshold() {
if ( _domain_structure_e_value_thr_exp < 3 ) {
_domain_structure_e_value_thr_exp += 1;
}
}
final private void increaseOvSize() {
if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 )
&& ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
.getHeight() / 2 ) ) {
setOvMaxWidth( getOvMaxWidth() + 5 );
setOvMaxHeight( getOvMaxHeight() + 5 );
updateOvSettings();
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
final void inferCommonPartOfScientificNames() {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
}
setWaitCursor();
Util.inferCommonPartOfScientificNames( _phylogeny );
setArrowCursor();
repaint();
}
final private void init() {
_color_chooser = new JColorChooser();
_rollover_popup = new JTextArea();
//******************************************START Changed**********************************************************//
// POPUP_FONT changed
if(AppletParams.isEitherTPorTDForLANLorBHB() || AppletParams.isArchaeopteryxForBHBorLANL()){
_rollover_popup.setFont( POPUP_FONT_NEW );
}
else {
_rollover_popup.setFont( POPUP_FONT );
}
//********************************************END**********************************************************//
resetNodeIdToDistToLeafMap();
setTextAntialias();
setTreeFile( null );
setEdited( false );
initializeOvSettings();
setStartingAngle( TWO_PI * 3 / 4 );
}
final private void initializeOvSettings() {
setOvMaxHeight( getConfiguration().getOvMaxHeight() );
setOvMaxWidth( getConfiguration().getOvMaxWidth() );
}
final void initNodeData() {
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
double max_original_domain_structure_width = 0.0;
for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
if ( node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
RenderableDomainArchitecture rds = null;
if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
getConfiguration() );
node.getNodeData().getSequence().setDomainArchitecture( rds );
}
else {
rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
}
if ( getControlPanel().isShowDomainArchitectures() ) {
final double dsw = rds.getOriginalSize().getWidth();
if ( dsw > max_original_domain_structure_width ) {
max_original_domain_structure_width = dsw;
}
}
}
}
if ( getControlPanel().isShowDomainArchitectures() ) {
final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
if ( node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
.getSequence().getDomainArchitecture();
rds.setRenderingFactorWidth( ds_factor_width );
rds.setParameter( _domain_structure_e_value_thr_exp );
}
}
}
}
final boolean inOv( final MouseEvent e ) {
return ( ( e.getX() > getVisibleRect().x + getOvXPosition() + 1 )
&& ( e.getX() < getVisibleRect().x + getOvXPosition() + getOvMaxWidth() - 1 )
&& ( e.getY() > getVisibleRect().y + getOvYPosition() + 1 ) && ( e.getY() < getVisibleRect().y
+ getOvYPosition() + getOvMaxHeight() - 1 ) );
}
final boolean inOvRectangle( final MouseEvent e ) {
return ( ( e.getX() >= getOvRectangle().getX() - 1 )
&& ( e.getX() <= getOvRectangle().getX() + getOvRectangle().getWidth() + 1 )
&& ( e.getY() >= getOvRectangle().getY() - 1 ) && ( e.getY() <= getOvRectangle().getY()
+ getOvRectangle().getHeight() + 1 ) );
}
final private boolean inOvVirtualRectangle( final int x, final int y ) {
return ( ( x >= getOvVirtualRectangle().x - 1 )
&& ( x <= getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 )
&& ( y >= getOvVirtualRectangle().y - 1 ) && ( y <= getOvVirtualRectangle().y
+ getOvVirtualRectangle().height + 1 ) );
}
final private boolean inOvVirtualRectangle( final MouseEvent e ) {
return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
}
final boolean isApplet() {
return getMainPanel() instanceof MainPanelApplets;
}
final private boolean isCanBlast( final PhylogenyNode node ) {
return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil
.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) )
|| !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node
.getNodeData().getSequence().getSymbol() ) ) );
}
final boolean isCanCollapse() {
return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
final boolean isCanColorSubtree() {
return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
final boolean isCanCopy() {
return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
}
final boolean isCanCut( final PhylogenyNode node ) {
return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
.isRoot() );
}
final boolean isCanDelete() {
return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
}
final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
if ( node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getAccession() != null )
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
&& getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
.toLowerCase() ) ) {
return true;
}
return false;
}
final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy()
&& ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
.isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
.getNodeData().getTaxonomy().getIdentifier() != null )
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
.getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
return true;
}
else {
return false;
}
}
final boolean isCanPaste() {
return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
&& ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
}
final boolean isCanReroot() {
return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
final boolean isCanSubtree( final PhylogenyNode node ) {
return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
.isRoot() || ( _subtree_index > 0 ) ) );
}
final boolean isEdited() {
return _edited;
}
final private boolean isInFoundNodes( final PhylogenyNode node ) {
return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node ) );
}
final private boolean isInOv() {
return _in_ov;
}
final boolean isInOvRect() {
return _in_ov_rect;
}
final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
return ( ( node.getYcoord() < getVisibleRect().getMinY() - 40 )
|| ( node.getYcoord() > getVisibleRect().getMaxY() + 40 ) || ( ( node.getParent() != null ) && ( node
.getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
}
final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
return ( ( node.getYcoord() < getVisibleRect().getMinY() - 20 )
|| ( node.getYcoord() > getVisibleRect().getMaxY() + 20 )
|| ( node.getXcoord() < getVisibleRect().getMinX() - 20 ) || ( node.getXcoord() > getVisibleRect()
.getMaxX() + 20 ) );
}
final private boolean isNonLinedUpCladogram() {
return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
}
final boolean isOvOn() {
return _ov_on;
}
final boolean isPhyHasBranchLengths() {
return _phy_has_branch_lengths;
}
final private boolean isUniformBranchLengthsForCladogram() {
return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
}
final private void keyPressedCalls( final KeyEvent e ) {
if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
if ( !isInOvRect() ) {
setInOvRect( true );
}
}
else if ( isInOvRect() ) {
setInOvRect( false );
}
}
if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
|| ( e.getKeyCode() == KeyEvent.VK_F ) ) {
getMainPanel().getTreeFontSet().mediumFonts();
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
getMainPanel().getTreeFontSet().decreaseFontSize();
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else if ( plusPressed( e.getKeyCode() ) ) {
getMainPanel().getTreeFontSet().increaseFontSize();
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
}
else {
if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
|| ( e.getKeyCode() == KeyEvent.VK_F ) ) {
getControlPanel().showWhole();
}
else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
|| ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
if ( e.getKeyCode() == KeyEvent.VK_UP ) {
getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
Constants.WHEEL_ZOOM_IN_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
final int d = 80;
int dx = 0;
int dy = -d;
if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
dy = d;
}
else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
dx = -d;
dy = 0;
}
else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
dx = d;
dy = 0;
}
final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
scroll_position.x = scroll_position.x + dx;
scroll_position.y = scroll_position.y + dy;
if ( scroll_position.x <= 0 ) {
scroll_position.x = 0;
}
else {
final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
if ( scroll_position.x >= max_x ) {
scroll_position.x = max_x;
}
}
if ( scroll_position.y <= 0 ) {
scroll_position.y = 0;
}
else {
final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
if ( scroll_position.y >= max_y ) {
scroll_position.y = max_y;
}
}
repaint();
getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
}
}
else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( plusPressed( e.getKeyCode() ) ) {
getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
Constants.WHEEL_ZOOM_IN_FACTOR );
getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getKeyCode() == KeyEvent.VK_S ) {
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else if ( e.getKeyCode() == KeyEvent.VK_A ) {
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
if ( getStartingAngle() < 0 ) {
setStartingAngle( TWO_PI + getStartingAngle() );
}
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else if ( e.getKeyCode() == KeyEvent.VK_D ) {
boolean selected = false;
if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
selected = true;
}
else {
getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
}
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
if ( ae.getlabelDirectionCbmi() != null ) {
ae.getlabelDirectionCbmi().setSelected( selected );
}
}
else {
getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
}
repaint();
}
else if ( e.getKeyCode() == KeyEvent.VK_X ) {
switchDisplaygetPhylogenyGraphicsType();
repaint();
}
else if ( e.getKeyCode() == KeyEvent.VK_C ) {
cycleColors();
repaint();
}
else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
MainFrame.cycleOverview( getOptions(), this );
repaint();
}
else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
increaseOvSize();
}
else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
decreaseOvSize();
}
e.consume();
}
}
final private void makePopupMenus( final PhylogenyNode node ) {
_node_popup_menu = new JPopupMenu();
final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
_node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
for( int i = 0; i < clickto_names.size(); i++ ) {
final String title = clickto_names.get( i );
_node_popup_menu_items[ i ] = new JMenuItem( title );
if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
if ( Constants.__RELEASE || Constants.__SNAPSHOT_RELEASE ) {
continue;
}
_node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
if ( !getOptions().isEditable() ) {
continue;
}
_node_popup_menu_items[ i ].setEnabled( isCanDelete() );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
if ( !getOptions().isEditable() ) {
continue;
}
_node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
if ( !getOptions().isEditable() ) {
continue;
}
_node_popup_menu_items[ i ].setEnabled( isCanCopy() );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
if ( !getOptions().isEditable() ) {
continue;
}
_node_popup_menu_items[ i ].setEnabled( isCanPaste() );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
if ( !getOptions().isEditable() ) {
continue;
}
}
else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
if ( !getOptions().isEditable() ) {
continue;
}
}
else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanReroot() );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanCollapse() );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
}
_node_popup_menu_items[ i ].addActionListener( this );
_node_popup_menu.add( _node_popup_menu_items[ i ] );
}
}
final void midpointRoot() {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
}
if ( !_phylogeny.isRerootable() ) {
JOptionPane.showMessageDialog( this,
"This is not rerootable",
"Not rerootable",
JOptionPane.WARNING_MESSAGE );
return;
}
setWaitCursor();
PhylogenyMethods.midpointRoot( _phylogeny );
resetNodeIdToDistToLeafMap();
setArrowCursor();
repaint();
}
final void mouseClicked( final MouseEvent e ) {
if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - getOvRectangle().getWidth() / 2.0 )
* w_ratio;
double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 )
* h_ratio;
if ( x < 0 ) {
x = 0;
}
if ( y < 0 ) {
y = 0;
}
final double max_x = getWidth() - getVisibleRect().width;
final double max_y = getHeight() - getVisibleRect().height;
if ( x > max_x ) {
x = max_x;
}
if ( y > max_y ) {
y = max_y;
}
getMainPanel().getCurrentScrollPane().getViewport()
.setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
setInOvRect( true );
repaint();
}
else {
final PhylogenyNode node = findNode( e.getX(), e.getY() );
if ( node != null ) {
if ( !node.isRoot() && node.getParent().isCollapse() ) {
return;
}
_highlight_node = node;
// Check if shift key is down
if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
// Yes, so add to _found_nodes
if ( getFoundNodes() == null ) {
setFoundNodes( new HashSet<PhylogenyNode>() );
}
getFoundNodes().add( node );
// Check if control key is down
}
else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
// Yes, so pop-up menu
displayNodePopupMenu( node, e.getX(), e.getY() );
// Handle unadorned click
}
else {
// Check for right mouse button
if ( e.getModifiers() == 4 ) {
displayNodePopupMenu( node, e.getX(), e.getY() );
}
else {
// if not in _found_nodes, clear _found_nodes
handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
}
}
}
else {
// no node was clicked
_highlight_node = null;
}
}
repaint();
}
final void mouseDragInBrowserPanel( final MouseEvent e ) {
setCursor( MOVE_CURSOR );
final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
scroll_position.x -= ( e.getX() - getLastDragPointX() );
scroll_position.y -= ( e.getY() - getLastDragPointY() );
if ( scroll_position.x < 0 ) {
scroll_position.x = 0;
}
else {
final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
if ( scroll_position.x > max_x ) {
scroll_position.x = max_x;
}
}
if ( scroll_position.y < 0 ) {
scroll_position.y = 0;
}
else {
final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
if ( scroll_position.y > max_y ) {
scroll_position.y = max_y;
}
}
if ( isOvOn() || getOptions().isShowScale() ) {
repaint();
}
getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
}
final void mouseDragInOvRectangle( final MouseEvent e ) {
setCursor( HAND_CURSOR );
final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
double dx = ( w_ratio * e.getX() - w_ratio * getLastDragPointX() );
double dy = ( h_ratio * e.getY() - h_ratio * getLastDragPointY() );
scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
if ( scroll_position.x <= 0 ) {
scroll_position.x = 0;
dx = 0;
}
else {
final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
if ( scroll_position.x >= max_x ) {
dx = 0;
scroll_position.x = max_x;
}
}
if ( scroll_position.y <= 0 ) {
dy = 0;
scroll_position.y = 0;
}
else {
final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
if ( scroll_position.y >= max_y ) {
dy = 0;
scroll_position.y = max_y;
}
}
repaint();
getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
}
final void mouseMoved( final MouseEvent e ) {
requestFocusInWindow();
if ( getControlPanel().isNodeDescPopup() ) {
if ( _node_desc_popup != null ) {
_node_desc_popup.hide();
_node_desc_popup = null;
}
}
if ( getOptions().isShowOverview() && isOvOn() ) {
if ( inOvVirtualRectangle( e ) ) {
if ( !isInOvRect() ) {
setInOvRect( true );
repaint();
}
}
else {
if ( isInOvRect() ) {
setInOvRect( false );
repaint();
}
}
}
if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
if ( !isInOv() ) {
setInOv( true );
}
}
else {
if ( isInOv() ) {
setInOv( false );
}
final PhylogenyNode node = findNode( e.getX(), e.getY() );
if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
// cursor is over a tree node
if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
|| ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
|| ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
|| ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
|| ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
|| ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
setCursor( CUT_CURSOR );
}
else {
setCursor( HAND_CURSOR );
if ( getControlPanel().isNodeDescPopup() ) {
showNodeDataPopup( e, node );
}
}
}
else {
setCursor( ARROW_CURSOR );
}
}
}
final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
setCursor( ARROW_CURSOR );
}
final public void mouseWheelMoved( final MouseWheelEvent e ) {
final int notches = e.getWheelRotation();
if ( inOvVirtualRectangle( e ) ) {
if ( !isInOvRect() ) {
setInOvRect( true );
repaint();
}
}
else {
if ( isInOvRect() ) {
setInOvRect( false );
repaint();
}
}
if ( e.isControlDown() ) {
if ( notches < 0 ) {
getTreeFontSet().increaseFontSize();
getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else {
getTreeFontSet().decreaseFontSize();
getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
}
else if ( e.isShiftDown() ) {
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
if ( notches < 0 ) {
for( int i = 0; i < ( -notches ); ++i ) {
setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
for( int i = 0; i < notches; ++i ) {
setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
if ( getStartingAngle() < 0 ) {
setStartingAngle( TWO_PI + getStartingAngle() );
}
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
}
else {
if ( notches < 0 ) {
for( int i = 0; i < ( -notches ); ++i ) {
getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
for( int i = 0; i < notches; ++i ) {
getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
}
}
else {
if ( notches < 0 ) {
for( int i = 0; i < ( -notches ); ++i ) {
getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
for( int i = 0; i < notches; ++i ) {
getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
}
requestFocus();
requestFocusInWindow();
requestFocus();
}
final void multiplyUrtFactor( final float f ) {
_urt_factor *= f;
}
final JApplet obtainApplet() {
return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
}
final private void openSeqWeb( final PhylogenyNode node ) {
if ( !isCanOpenSeqWeb( node ) ) {
cannotOpenBrowserWarningMessage( "sequence" );
return;
}
String uri_str = null;
final Sequence seq = node.getNodeData().getSequence();
final String source = seq.getAccession().getSource().toLowerCase();
String url;
if ( source.toLowerCase().equals( "ncbi" ) ) {
url = Constants.NCBI_ALL_DATABASE_SEARCH;
}
else {
final WebLink weblink = getConfiguration().getWebLink( source );
url = weblink.getUrl().toString();
}
try {
uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
JApplet applet = null;
if ( isApplet() ) {
applet = obtainApplet();
}
Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
}
catch ( final IOException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
catch ( final URISyntaxException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
else {
cannotOpenBrowserWarningMessage( "sequence" );
}
}
final private void openTaxWeb( final PhylogenyNode node ) {
if ( !isCanOpenTaxWeb( node ) ) {
cannotOpenBrowserWarningMessage( "taxonomic" );
return;
}
String uri_str = null;
final Taxonomy tax = node.getNodeData().getTaxonomy();
if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
&& getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
final String type = tax.getIdentifier().getProvider().toLowerCase();
final WebLink weblink = getConfiguration().getWebLink( type );
try {
uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
&& tax.getIdentifier().getValue().startsWith( "http://" ) ) {
try {
uri_str = new URI( tax.getIdentifier().getValue() ).toString();
}
catch ( final URISyntaxException e ) {
Util.showErrorMessage( this, e.toString() );
uri_str = null;
e.printStackTrace();
}
}
else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
try {
uri_str = "http://www.eol.org/search?q="
+ URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
try {
uri_str = "http://www.eol.org/search?q="
+ URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
JApplet applet = null;
if ( isApplet() ) {
applet = obtainApplet();
}
Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
}
catch ( final IOException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
catch ( final URISyntaxException e ) {
Util.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
else {
cannotOpenBrowserWarningMessage( "taxonomic" );
}
}
final void paintBranchCircular( final PhylogenyNode p,
final PhylogenyNode c,
final Graphics2D g,
final boolean radial_labels,
final boolean to_pdf,
final boolean to_graphics_file ) {
final double angle = _urt_nodeid_angle_map.get( c.getNodeId() );
final double root_x = _root.getXcoord();
final double root_y = _root.getYcoord();
final double dx = root_x - p.getXcoord();
final double dy = root_y - p.getYcoord();
final double parent_radius = Math.sqrt( dx * dx + dy * dy );
final double arc = ( _urt_nodeid_angle_map.get( p.getNodeId() ) ) - angle;
assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
if ( ( c.isFirstChildNode() || c.isLastChildNode() )
&& ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
final double r2 = 2.0 * parent_radius;
drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
}
drawLine( c.getXcoord(), c.getYcoord(), root_x + ( Math.cos( angle ) * parent_radius ), root_y
+ ( Math.sin( angle ) * parent_radius ), g );
paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) );
if ( c.isExternal() ) {
final boolean is_in_found_nodes = isInFoundNodes( c );
if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
&& ( _urt_nodeid_index_map.get( c.getNodeId() ) % _dynamic_hiding_factor != 1 ) ) {
return;
}
paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
}
}
final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
final double angle = _urt_nodeid_angle_map.get( c.getNodeId() );
final double root_x = _root.getXSecondary();
final double root_y = _root.getYSecondary();
final double dx = root_x - p.getXSecondary();
final double dy = root_y - p.getYSecondary();
final double arc = ( _urt_nodeid_angle_map.get( p.getNodeId() ) ) - angle;
final double parent_radius = Math.sqrt( dx * dx + dy * dy );
g.setColor( getTreeColorSet().getOvColor() );
if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
final double r2 = 2.0 * parent_radius;
drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
}
drawLine( c.getXSecondary(), c.getYSecondary(), root_x + ( Math.cos( angle ) * parent_radius ), root_y
+ ( Math.sin( angle ) * parent_radius ), g );
if ( isInFoundNodes( c ) ) {
g.setColor( getTreeColorSet().getFoundColor() );
drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
}
}
final private void paintBranchLength( final Graphics2D g,
final PhylogenyNode node,
final boolean to_pdf,
final boolean to_graphics_file ) {
g.setFont( getTreeFontSet().getSmallFont() );
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else {
g.setColor( getTreeColorSet().getBranchLengthColor() );
}
if ( !node.isRoot() ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
.getXcoord()
+ EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
.getXcoord()
+ ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
.getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
}
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- getTreeFontSet()._small_max_descent, g );
}
}
final private void paintBranchLite( final Graphics2D g,
final float x1,
final float x2,
final float y1,
final float y2,
final PhylogenyNode node ) {
g.setColor( getTreeColorSet().getOvColor() );
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
drawLine( x1, y1, x2, y2, g );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
_quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
( g ).draw( _quad_curve );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
final float dx = x2 - x1;
final float dy = y2 - y1;
_cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
+ ( dy * 0.8f ), x2, y2 );
( g ).draw( _cubic_curve );
}
else {
final float x2a = x2;
final float x1a = x1;
// draw the vertical line
if ( node.isFirstChildNode() || node.isLastChildNode() ) {
drawLine( x1, y1, x1, y2, g );
}
// draw the horizontal line
drawLine( x1a, y2, x2a, y2, g );
}
}
/**
* Paint a branch which consists of a vertical and a horizontal bar
* @param is_ind_found_nodes
*/
final private void paintBranchRectangular( final Graphics2D g,
final float x1,
final float x2,
float y1,
final float y2,
final PhylogenyNode node,
final boolean to_pdf,
final boolean to_graphics_file ) {
assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
drawLine( x1, y1, x2, y2, g );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
_quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
g.draw( _quad_curve );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
final float dx = x2 - x1;
final float dy = y2 - y1;
_cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
+ ( dy * 0.8f ), x2, y2 );
g.draw( _cubic_curve );
}
else {
float x2a = x2;
float x1a = x1;
// draw the vertical line
boolean draw_horizontal = true;
float y2_r = 0;
if ( node.isFirstChildNode() || node.isLastChildNode()
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
boolean draw_vertical = true;
final PhylogenyNode parent = node.getParent();
if ( ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
.isEvents() )
&& ( parent != null ) && parent.isHasAssignedEvent() ) )
&& ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
&& !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
.isDuplication() ) ) {
if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
&& ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( Math.abs( y2 - y1 ) <= TreePanel.HALF_BOX_SIZE ) {
draw_vertical = false;
}
else {
if ( y1 < y2 ) {
y1 += TreePanel.HALF_BOX_SIZE;
}
else {
if ( !to_pdf ) {
y1 -= TreePanel.HALF_BOX_SIZE + 1;
}
else {
y1 -= TreePanel.HALF_BOX_SIZE;
}
}
}
}
if ( ( x2 - x1 ) <= TreePanel.HALF_BOX_SIZE ) {
draw_horizontal = false;
}
else if ( !draw_vertical ) {
x1a += TreePanel.HALF_BOX_SIZE;
}
if ( ( ( x2 - x1a ) > TreePanel.HALF_BOX_SIZE )
&& !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
.isDuplication() ) ) {
x2a -= TreePanel.HALF_BOX_SIZE;
}
}
if ( draw_vertical ) {
if ( !to_graphics_file
&& !to_pdf
&& ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
.getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
// Do nothing.
}
else {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
float x2c = x1 + EURO_D;
if ( x2c > x2a ) {
x2c = x2a;
}
drawLine( x1, y1, x2c, y2, g );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
if ( y2 > y1 ) {
y2_r = y2 - ROUNDED_D;
if ( y2_r < y1 ) {
y2_r = y1;
}
drawLine( x1, y1, x1, y2_r, g );
}
else {
y2_r = y2 + ROUNDED_D;
if ( y2_r > y1 ) {
y2_r = y1;
}
drawLine( x1, y1, x1, y2_r, g );
}
}
else {
drawLine( x1, y1, x1, y2, g );
}
}
}
}
// draw the horizontal line
if ( !to_graphics_file && !to_pdf
&& ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) {
return;
}
float x1_r = 0;
if ( draw_horizontal ) {
if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
x1_r = x1a + ROUNDED_D;
if ( x1_r < x2a ) {
drawLine( x1_r, y2, x2a, y2, g );
}
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
final float x1c = x1a + EURO_D;
if ( x1c < x2a ) {
drawLine( x1c, y2, x2a, y2, g );
}
}
else {
//drawLine( x1a, y2, x2a, y2, g );
//******************************************START CHANGED**********************************************************//
if(AppletParams.isTreePrunerForAll() ){
treePrunerPaint.drawThickLine(g,node, x1a, y2, x2a, y2);
}
else{
drawLine( x1a, y2, x2a, y2, g );
}
//Commented changed
//********************************************END**********************************************************//
}
}
else {
final double w = PhylogenyMethods.getBranchWidthValue( node );
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
x1_r = x1a + ROUNDED_D;
if ( x1_r < x2a ) {
drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
}
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
final float x1c = x1a + EURO_D;
if ( x1c < x2a ) {
drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
}
}
else {
drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
}
}
}
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( x1_r > x2a ) {
x1_r = x2a;
}
if ( y2 > y2_r ) {
final double diff = y2 - y2_r;
_arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
}
else {
_arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
}
g.draw( _arc );
}
}
paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
}
final void paintCircular( final Phylogeny phy,
final double starting_angle,
final int center_x,
final int center_y,
final int radius,
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file ) {
_circ_num_ext_nodes = phy.getNumberOfExternalNodes();
_root = phy.getRoot();
_root.setXcoord( center_x );
_root.setYcoord( center_y );
paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
double current_angle = starting_angle;
int i = 0;
for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
_urt_nodeid_angle_map.put( n.getNodeId(), current_angle );
_urt_nodeid_index_map.put( n.getNodeId(), i++ );
current_angle += ( TWO_PI / _circ_num_ext_nodes );
}
paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
}
final void paintCircularLite( final Phylogeny phy,
final double starting_angle,
final int center_x,
final int center_y,
final int radius,
final Graphics2D g ) {
_circ_num_ext_nodes = phy.getNumberOfExternalNodes();
_root = phy.getRoot();
_root.setXSecondary( center_x );
_root.setYSecondary( center_y );
double current_angle = starting_angle;
for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
_urt_nodeid_angle_map.put( n.getNodeId(), current_angle );
current_angle += ( TWO_PI / _circ_num_ext_nodes );
}
paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
}
final private double paintCirculars( final PhylogenyNode n,
final Phylogeny phy,
final float center_x,
final float center_y,
final double radius,
final boolean radial_labels,
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file ) {
if ( n.isExternal() ) {
return _urt_nodeid_angle_map.get( n.getNodeId() );
}
else {
final List<PhylogenyNode> descs = n.getDescendants();
double sum = 0;
for( final PhylogenyNode desc : descs ) {
sum += paintCirculars( desc,
phy,
center_x,
center_y,
radius,
radial_labels,
g,
to_pdf,
to_graphics_file );
}
double r = 0;
if ( !n.isRoot() ) {
r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
}
final double theta = sum / descs.size();
n.setXcoord( ( float ) ( center_x + r * radius * Math.cos( theta ) ) );
n.setYcoord( ( float ) ( center_y + r * radius * Math.sin( theta ) ) );
_urt_nodeid_angle_map.put( n.getNodeId(), theta );
for( final PhylogenyNode desc : descs ) {
paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
}
return theta;
}
}
final private void paintCircularsLite( final PhylogenyNode n,
final Phylogeny phy,
final int center_x,
final int center_y,
final int radius,
final Graphics2D g ) {
if ( n.isExternal() ) {
return;
}
else {
final List<PhylogenyNode> descs = n.getDescendants();
for( final PhylogenyNode desc : descs ) {
paintCircularsLite( desc, phy, center_x, center_y, radius, g );
}
float r = 0;
if ( !n.isRoot() ) {
r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
}
final double theta = _urt_nodeid_angle_map.get( n.getNodeId() );
n.setXSecondary( ( float ) ( center_x + radius * r * Math.cos( theta ) ) );
n.setYSecondary( ( float ) ( center_y + radius * r * Math.sin( theta ) ) );
for( final PhylogenyNode desc : descs ) {
paintBranchCircularLite( n, desc, g );
}
}
}
final private void paintCollapsedNode( final Graphics2D g,
final PhylogenyNode node,
final boolean to_graphics_file,
final boolean to_pdf,
final boolean is_in_found_nodes ) {
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
g.setColor( getTreeColorSet().getFoundColor() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
g.setColor( getTreeColorSet().getCollapseFillColor() );
}
double d = node.getAllExternalDescendants().size();
if ( d > 1000 ) {
d = ( 3 * _y_distance ) / 3;
}
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
if ( d < BOX_SIZE ) {
d = BOX_SIZE;
}
_polygon.reset();
_polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ), ForesterUtil
.roundToInt( node.getYcoord() ) );
_polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), ForesterUtil
.roundToInt( node.getYcoord() - d ) );
_polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), ForesterUtil
.roundToInt( node.getYcoord() + d ) );
g.fillPolygon( _polygon );
paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
@Override
final public void paintComponent( final Graphics g ) {
// Dimension currentSize = getSize();
// if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
// call the 'java.awt.Component.createImage(...)' method to get an
// image
// offscreenImage = createImage( currentSize.width, currentSize.height );
// offscreenGraphics = offscreenImage.getGraphics();
// offscreenDimension = currentSize;
// }
// super.paintComponent( g ); //why?
//final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
final Graphics2D g2d = ( Graphics2D ) g;
g2d.setRenderingHints( _rendering_hints );
paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
//g.drawImage( offscreenImage, 0, 0, this );
}
@Override
public void update( final Graphics g ) {
paint( g );
}
final private void paintConfidenceValues( final Graphics2D g,
final PhylogenyNode node,
final boolean to_pdf,
final boolean to_graphics_file ) {
String conf_str = "";
final List<Confidence> confidences = node.getBranchData().getConfidences();
if ( confidences.size() == 1 ) {
final double value = node.getBranchData().getConfidence( 0 ).getValue();
if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
return;
}
conf_str = FORMATTER_CONFIDENCE.format( value );
}
else if ( confidences.size() > 1 ) {
boolean one_ok = false;
boolean not_first = false;
Collections.sort( confidences );
final StringBuilder sb = new StringBuilder();
for( final Confidence confidence : confidences ) {
final double value = confidence.getValue();
if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
if ( value >= getOptions().getMinConfidenceValue() ) {
one_ok = true;
}
if ( not_first ) {
sb.append( "/" );
}
else {
not_first = true;
}
sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
.getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
}
}
if ( one_ok ) {
conf_str = sb.toString();
}
}
if ( conf_str.length() > 0 ) {
final double parent_x = node.getParent().getXcoord();
double x = node.getXcoord();
g.setFont( getTreeFontSet().getSmallFont() );
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
x += EURO_D;
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
x += ROUNDED_D;
}
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else {
g.setColor( getTreeColorSet().getConfidenceColor() );
}
TreePanel
.drawString( conf_str, parent_x
+ ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ), ( node
.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1, g );
}
}
final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
g.setColor( getTreeColorSet().getFoundColor() );
g.fillRect( x - TreePanel.HALF_BOX_SIZE, y - TreePanel.HALF_BOX_SIZE, TreePanel.BOX_SIZE, TreePanel.BOX_SIZE );
}
final private void paintGainedAndLostCharacters( final Graphics2D g,
final PhylogenyNode node,
final String gained,
final String lost ) {
if ( node.getParent() != null ) {
final double parent_x = node.getParent().getXcoord();
final double x = node.getXcoord();
g.setFont( getTreeFontSet().getLargeFont() );
g.setColor( getTreeColorSet().getGainedCharactersColor() );
if ( Constants.SPECIAL_CUSTOM ) {
g.setColor( Color.BLUE );
}
TreePanel
.drawString( gained, parent_x
+ ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ), ( node
.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ) - 1, g );
g.setColor( getTreeColorSet().getLostCharactersColor() );
TreePanel.drawString( lost,
parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ) + 1,
g );
}
}
/**
* Draw a box at the indicated node.
*
* @param x
* @param y
* @param node
* @param g
*/
final private void paintNodeBox( final double x,
final double y,
final PhylogenyNode node,
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file,
final boolean is_in_found_nodes ) {
if ( node.isCollapse() ) {
return;
}
// if this node should be highlighted, do so
if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
g.setColor( getTreeColorSet().getFoundColor() );
drawOval( x - 8, y - 8, 16, 16, g );
drawOval( x - 9, y - 8, 17, 17, g );
drawOval( x - 9, y - 9, 18, 18, g );
}
//******************************************START**********************************************************//
if(AppletParams.isEitherTPorTDForAll()){
newWindowSubtree.paintNodeTracker(g, x, y, node, to_pdf, to_graphics_file);
}
if(AppletParams.isTreeDecoratorForAll()){
_control_panel.controlPanelAdditions.callTreeDecoratorAutoSaveToRefresh();
if ( is_in_found_nodes ) {
paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
}
else if ( getOptions().isShowNodeBoxes()){
treeDecoratorPaint.decorateNodeBox(g, ForesterUtil.roundToInt(x), ForesterUtil.roundToInt(y), node);
}
}
else{
//********************************************END**********************************************************//
if ( is_in_found_nodes ) {
paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
}
else {
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
g.setColor( getTreeColorSet().getDuplicationBoxColor() );
}
else if ( event.isSpeciation() ) {
g.setColor( getTreeColorSet().getSpecBoxColor() );
}
else if ( event.isSpeciationOrDuplication() ) {
g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() );
}
}
else {
assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
}
if ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file )
|| ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
if ( to_pdf || to_graphics_file ) {
if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
drawOvalFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
}
}
else {
drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
}
}
//******************************************START**********************************************************//
}
//********************************************END**********************************************************//
}
}
final private void paintNodeData( final Graphics2D g,
final PhylogenyNode node,
final boolean to_graphics_file,
final boolean to_pdf,
final boolean is_in_found_nodes ) {
if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
return;
}
if ( getOptions().isShowBranchLengthValues()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
&& ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) {
paintBranchLength( g, node, to_pdf, to_graphics_file );
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
return;
}
int x = 0;
if ( node.getNodeData().isHasTaxonomy()
&& ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
.isShowTaxonomyCommonNames() ) ) {
x = paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file );
}
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
g.setColor( getTreeColorSet().getFoundColor() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
else if ( to_pdf ) {
g.setColor( Color.BLACK );
}
else {
g.setColor( getTreeColorSet().getSequenceColor() );
}
_sb.setLength( 0 );
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
_sb.append( " [" );
_sb.append( node.getAllExternalDescendants().size() );
_sb.append( "]" );
}
if ( getControlPanel().isShowNodeNames() && ( node.getNodeName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
//_sb.append( node.getNodeName() );
//******************************************START CHANGED**********************************************************//
if(AppletParams.isEitherTPorTDForAll()){
_sb.append(Accession.removeAccessionFromStrain(node));
}
else{
_sb.append( node.getNodeName() );
}
//commented changed
//********************************************END**********************************************************//
}
if ( node.getNodeData().isHasSequence() ) {
if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
_sb.append( node.getNodeData().getSequence().getSymbol() );
}
if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
_sb.append( node.getNodeData().getSequence().getName() );
}
if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
_sb.append( node.getNodeData().getSequence().getAccession().getSource() );
_sb.append( ":" );
}
_sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
}
//******************************************START**********************************************************//
if(AppletParams.isTreePrunerForAll() ){
treePrunerPaint.initArrayLists();
treePrunerPaint.paintKeepRemove(g,node);
}
//********************************************END**********************************************************//
g.setFont( getTreeFontSet().getLargeFont() );
if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
}
double down_shift_factor = 3.0;
if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
down_shift_factor = 1;
}
// GUILHEM_BEG ______________
final double posX = node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE;
final double posY = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
final int CONFIDENCE_LEFT_MARGIN = 4;
final String sNodeText = _sb.toString();
if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
&& ( _query_sequence != null ) ) {
int nodeTextBoundsWidth = 0;
if ( sNodeText.length() > 0 ) {
final Rectangle2D node_text_bounds = new TextLayout( sNodeText, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
}
if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
g.fillRect( ( int ) posX - 1, ( int ) posY - 8, nodeTextBoundsWidth + 5, 11 );
g.setColor( getTreeColorSet().getBackgroundColor() );
}
}
else {
final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
for( final SequenceRelation seqRelation : seqRelations ) {
final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
.getRef1().isEqual( _query_sequence ) )
&& seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
.getSelectedItem() );
if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
final double linePosX = node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE;
final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
.getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
+ ")";
if ( sConfidence != null ) {
double confidenceX = posX;
if ( sNodeText.length() > 0 ) {
confidenceX += new TextLayout( sNodeText, g.getFont(), _frc ).getBounds().getWidth()
+ CONFIDENCE_LEFT_MARGIN;
}
if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
.getBounds().getWidth();
TreePanel.drawString( sConfidence, confidenceX, posY, g );
x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
}
}
if ( x + nodeTextBoundsWidth > 0 ) /* we only underline if there is something displayed */
{
if ( nodeTextBoundsWidth == 0 ) {
nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
}
else {
nodeTextBoundsWidth += 2;
}
g.drawLine( ( int ) linePosX + 1, 3 + ( int ) posY, ( int ) linePosX + x
+ nodeTextBoundsWidth, 3 + ( int ) posY );
break;
}
}
}
}
}
if ( sNodeText.length() > 0 ) {
//******************************************START**********************************************************//
// TODO Check for consistency
if(AppletParams.isTreeDecoratorForAll()){
if ( is_in_found_nodes ) {
g.setColor( getTreeColorSet().getFoundColor() );
g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
}
else{
treeDecoratorPaint.decorateStrain(g, ForesterUtil.roundToInt
(node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE),
ForesterUtil.roundToInt(node.getYcoord()+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor))
, _sb.toString(), node,to_pdf);
}
}
else
//********************************************END**********************************************************//
TreePanel.drawString( sNodeText, posX, posY, g );
}
// GUILHEM_END _____________
// COMMENTED_OUT_BY_GUILHEM_BEG _______________
// TODO FIXME need to check this one!
//if ( _sb.length() > 0 ) {
// TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
// + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
//}
// COMMENTED_OUT_BY_GUILHEM_END ________________
if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
if ( _sb.length() > 0 ) {
x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
}
final Annotation ann = ( Annotation ) node.getNodeData().getSequence().getAnnotations().get( 0 );
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else {
g.setColor( calculateColorForAnnotation( ann ) );
}
final String ann_str = ann.asSimpleText().toString();
TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
_sb.append( ann_str );
}
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
&& node.getNodeData().isHasBinaryCharacters() ) {
if ( _sb.length() > 0 ) {
x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
}
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else {
g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
}
if ( getControlPanel().isShowBinaryCharacters() ) {
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
.toString(), node.getXcoord() + x + 1 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
.getLostCharactersAsStringBuffer().toString() );
}
else {
if ( DRAW_MEAN_COUNTS && node.isInternal() ) {
final List<PhylogenyNode> ec = node.getAllExternalDescendants();
double sum = 0;
int count = 0;
for( final PhylogenyNode phylogenyNode : ec ) {
count++;
if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) {
sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount();
}
}
final double mean = ForesterUtil.round( sum / count, 1 );
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCount() + " [" + mean
+ "]", node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
}
else {
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCount(), node
.getXcoord()
+ x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
}
paintGainedAndLostCharacters( g, node, "+"
+ node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
+ node.getNodeData().getBinaryCharacters().getLostCount() );
}
}
}
}
final private void paintNodeDataUnrootedCirc( final Graphics2D g,
final PhylogenyNode node,
final boolean to_pdf,
final boolean to_graphics_file,
final boolean radial_labels,
final double ur_angle,
final boolean is_in_found_nodes ) {
if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
return;
}
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
g.setColor( getTreeColorSet().getFoundColor() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
else {
g.setColor( getTreeColorSet().getSequenceColor() );
}
_sb.setLength( 0 );
_sb.append( " " );
if ( node.getNodeData().isHasTaxonomy()
&& ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
.isShowTaxonomyCommonNames() ) ) {
final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
_sb.append( taxonomy.getTaxonomyCode() );
_sb.append( " " );
}
if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
&& !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
_sb.append( taxonomy.getScientificName() );
_sb.append( " (" );
_sb.append( taxonomy.getCommonName() );
_sb.append( ") " );
}
else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
_sb.append( taxonomy.getScientificName() );
_sb.append( " " );
}
else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
_sb.append( taxonomy.getCommonName() );
_sb.append( " " );
}
}
else if ( _control_panel.isShowTaxonomyScientificNames() ) {
if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
_sb.append( taxonomy.getScientificName() );
_sb.append( " " );
}
}
else if ( _control_panel.isShowTaxonomyCommonNames() ) {
if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
_sb.append( taxonomy.getCommonName() );
_sb.append( " " );
}
}
}
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
_sb.append( " [" );
_sb.append( node.getAllExternalDescendants().size() );
_sb.append( "]" );
}
if ( getControlPanel().isShowNodeNames() && ( node.getNodeName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
_sb.append( node.getNodeName() );
}
if ( node.getNodeData().isHasSequence() ) {
if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
_sb.append( node.getNodeData().getSequence().getAccession().getSource() );
_sb.append( ":" );
}
_sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
_sb.append( node.getNodeData().getSequence().getName() );
}
}
g.setFont( getTreeFontSet().getLargeFont() );
if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
}
if ( _sb.length() > 1 ) {
final String sb_str = _sb.toString();
double m = 0;
if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
m = _urt_nodeid_angle_map.get( node.getNodeId() ) % TWO_PI;
}
else {
m = ( float ) ( ur_angle % TWO_PI );
}
_at = g.getTransform();
boolean need_to_reset = false;
final float x_coord = node.getXcoord();
final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
if ( radial_labels ) {
need_to_reset = true;
boolean left = false;
if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
m -= PI;
left = true;
}
g.rotate( m, x_coord, node.getYcoord() );
if ( left ) {
g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
}
}
else {
if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
need_to_reset = true;
g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
}
}
TreePanel.drawString( sb_str, x_coord, y_coord, g );
if ( need_to_reset ) {
g.setTransform( _at );
}
}
}
final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
if ( node.isCollapse() ) {
if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
paintCollapsedNode( g, node, false, false, false );
}
return;
}
if ( isInFoundNodes( node ) ) {
g.setColor( getTreeColorSet().getFoundColor() );
drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
}
float new_x = 0;
if ( !node.isExternal() && !node.isCollapse() ) {
boolean first_child = true;
float y2 = 0.0f;
final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
final PhylogenyNode child_node = node.getChildNode( i );
int factor_x;
if ( !isUniformBranchLengthsForCladogram() ) {
factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
}
else {
factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
}
if ( first_child ) {
first_child = false;
y2 = node.getYSecondary()
- ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
.getNumberOfExternalNodes() ) );
}
else {
y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
}
final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
new_x = x2 + node.getXSecondary();
final float diff_y = node.getYSecondary() - y2;
final float diff_x = node.getXSecondary() - new_x;
if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
}
child_node.setXSecondary( new_x );
child_node.setYSecondary( y2 );
y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
}
}
}
final private void paintNodeRectangular( final Graphics2D g,
final PhylogenyNode node,
final boolean to_pdf,
final boolean dynamically_hide,
final int dynamic_hiding_factor,
final boolean to_graphics_file ) {
final boolean is_in_found_nodes = isInFoundNodes( node );
if ( node.isCollapse() ) {
if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
return;
}
if ( node.isExternal() ) {
++_external_node_index;
}
// Confidence values
if ( getControlPanel().isShowBootstrapValues()
&& !node.isExternal()
&& !node.isRoot()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
&& node.getBranchData().isHasConfidences() ) {
paintConfidenceValues( g, node, to_pdf, to_graphics_file );
}
// Draw a line to root:
if ( node.isRoot() && _phylogeny.isRooted() ) {
paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
}
float new_x = 0;
float new_x_min = Float.MAX_VALUE;
final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
float min_dist = 1.5f;
if ( !disallow_shortcutting ) {
// System.out.println( dynamic_hiding_factor );
if ( dynamic_hiding_factor > 4000 ) {
min_dist = 4;
}
else if ( dynamic_hiding_factor > 1000 ) {
min_dist = 3;
}
else if ( dynamic_hiding_factor > 100 ) {
min_dist = 2;
}
}
if ( !node.isExternal() && !node.isCollapse() ) {
boolean first_child = true;
float y2 = 0.0f;
final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
final PhylogenyNode child_node = node.getChildNode( i );
int factor_x;
if ( !isUniformBranchLengthsForCladogram() ) {
factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
}
else {
factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
}
if ( first_child ) {
first_child = false;
y2 = node.getYcoord()
- ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
}
else {
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
final float x2 = calculateBranchLengthToParent( child_node, factor_x );
new_x = x2 + node.getXcoord();
if ( dynamically_hide && ( x2 < new_x_min ) ) {
new_x_min = x2;
}
final float diff_y = node.getYcoord() - y2;
final float diff_x = node.getXcoord() - new_x;
if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
|| ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
paintBranchRectangular( g,
node.getXcoord(),
new_x,
node.getYcoord(),
y2,
child_node,
to_pdf,
to_graphics_file );
}
child_node.setXcoord( new_x );
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
}
if ( dynamically_hide
&& !is_in_found_nodes
&& ( ( node.isExternal() && ( _external_node_index % dynamic_hiding_factor != 1 ) ) || ( !node
.isExternal() && ( ( new_x_min < 20 ) || ( _y_distance * node.getNumberOfExternalNodes() < getTreeFontSet()._fm_large
.getHeight() ) ) ) ) ) {
return;
}
paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
}
final private void paintNodeWithRenderableData( final Graphics2D g,
final PhylogenyNode node,
final boolean to_graphics_file,
final boolean to_pdf ) {
if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
return;
}
if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
return;
}
if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
RenderableDomainArchitecture rds = null;
try {
rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
}
catch ( final ClassCastException cce ) {
return;
}
rds.setRenderingHeight( 6 );
int x = 0;
if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) {
x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
}
if ( getControlPanel().isShowNodeNames() && ( node.getNodeName().length() > 0 ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getNodeName() + " " );
}
rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
}
}
final private void paintOvRectangle( final Graphics2D g ) {
final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
final float width = getOvMaxWidth() / w_ratio;
final float height = getOvMaxHeight() / h_ratio;
final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio;
final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio;
g.setColor( getTreeColorSet().getFoundColor() );
getOvRectangle().setRect( x, y, width, height );
if ( ( width < 6 ) && ( height < 6 ) ) {
drawRectFilled( x, y, 6, 6, g );
getOvVirtualRectangle().setRect( x, y, 6, 6 );
}
else if ( width < 6 ) {
drawRectFilled( x, y, 6, height, g );
getOvVirtualRectangle().setRect( x, y, 6, height );
}
else if ( height < 6 ) {
drawRectFilled( x, y, width, 6, g );
getOvVirtualRectangle().setRect( x, y, width, 6 );
}
else {
drawRect( x, y, width, height, g );
if ( isInOvRect() ) {
drawRect( x + 1, y + 1, width - 2, height - 2, g );
}
getOvVirtualRectangle().setRect( x, y, width, height );
}
}
//******************************************START CHANGED**********************************************************//
public void paintPhylogeny( final Graphics2D g,
// void paintPhylogeny( finalvoid Graphics2D g, // default->public - changed
//********************************************END**********************************************************//
final boolean to_pdf,
final boolean to_graphics_file,
final int graphics_file_width,
final int graphics_file_height,
final int graphics_file_x,
final int graphics_file_y ) {
/* GUILHEM_BEG */
// System.out.println( "p" + ( xxx++ ) );
_query_sequence = _control_panel.getSelectedQuerySequence();
/* GUILHEM_END */
// Color the background
if ( !to_pdf ) {
//******************************************START CHANGED**********************************************************//
/* if(AppletParams.isTreePrunerForAll() ){
g.setColor(TreePrunerColorSet.getBackgroundColor());
}
else if(AppletParams.isTreeDecoratorForAll() ){
g.setColor(DecoratorColorSet.getBackgroundColor());
}
else{*/
g.setColor( getTreeColorSet().getBackgroundColor() );
/*}*/
// //Changed the background color from Back to white - changed
//********************************************END**********************************************************//
final Rectangle r = getVisibleRect();
if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
g.setColor( getTreeColorSet().getBackgroundColor() );
if ( !to_graphics_file ) {
g.fill( r );
}
else {
if ( getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.WHITE );
}
g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
}
}
else {
if ( !to_graphics_file ) {
g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
+ r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
g.fill( r );
}
else {
g.setPaint( new GradientPaint( graphics_file_x,
graphics_file_y,
getTreeColorSet().getBackgroundColor(),
graphics_file_x,
graphics_file_y + graphics_file_height,
getTreeColorSet().getBackgroundColorGradientBottom() ) );
g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
}
}
g.setStroke( new BasicStroke( 1 ) );
}
else {
g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
}
if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
&& ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
_external_node_index = 0;
// Position starting X of tree
if ( !_phylogeny.isRooted() ) {
_phylogeny.getRoot().setXcoord( TreePanel.MOVE );
}
else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
_phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
.getDistanceToParent() * getXcorrectionFactor() ) ) );
}
else {
_phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
}
// Position starting Y of tree
_phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
+ ( TreePanel.MOVE / 2.0f ) );
final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
if ( getControlPanel().isDynamicallyHideData() ) {
if ( dynamic_hiding_factor > 1 ) {
getControlPanel().setDynamicHidingIsOn( true );
}
else {
getControlPanel().setDynamicHidingIsOn( false );
}
}
final PhylogenyNodeIterator it;
for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
&& ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
}
if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
if ( !( to_graphics_file || to_pdf ) ) {
paintScale( g,
getVisibleRect().x,
getVisibleRect().y + getVisibleRect().height,
to_pdf,
to_graphics_file );
}
else {
paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
}
}
if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
paintPhylogenyLite( g );
}
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
if ( getControlPanel().getDynamicallyHideData() != null ) {
getControlPanel().setDynamicHidingIsOn( false );
}
final double angle = getStartingAngle();
final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
_dynamic_hiding_factor = 0;
if ( getControlPanel().isDynamicallyHideData() ) {
_dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
.getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
}
if ( getControlPanel().getDynamicallyHideData() != null ) {
if ( _dynamic_hiding_factor > 1 ) {
getControlPanel().setDynamicHidingIsOn( true );
}
else {
getControlPanel().setDynamicHidingIsOn( false );
}
}
paintUnrooted( _phylogeny.getRoot(),
angle,
( float ) ( angle + 2 * Math.PI ),
radial_labels,
g,
to_pdf,
to_graphics_file );
if ( getOptions().isShowScale() ) {
if ( !( to_graphics_file || to_pdf ) ) {
paintScale( g,
getVisibleRect().x,
getVisibleRect().y + getVisibleRect().height,
to_pdf,
to_graphics_file );
}
else {
paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
}
}
if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
g.setColor( getTreeColorSet().getOvColor() );
paintUnrootedLite( _phylogeny.getRoot(),
angle,
angle + 2 * Math.PI,
g,
( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
paintOvRectangle( g );
}
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
final int d = radius + MOVE + getLongestExtNodeInfo();
_dynamic_hiding_factor = 0;
if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
_dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
.getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
}
if ( getControlPanel().getDynamicallyHideData() != null ) {
if ( _dynamic_hiding_factor > 1 ) {
getControlPanel().setDynamicHidingIsOn( true );
}
else {
getControlPanel().setDynamicHidingIsOn( false );
}
}
paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
: getOvMaxWidth() / 2 );
double x_scale = 1.0;
double y_scale = 1.0;
int x_pos = getVisibleRect().x + getOvXPosition();
int y_pos = getVisibleRect().y + getOvYPosition();
if ( getWidth() > getHeight() ) {
x_scale = ( double ) getHeight() / getWidth();
x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
}
else {
y_scale = ( double ) getWidth() / getHeight();
y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
}
_at = g.getTransform();
g.scale( x_scale, y_scale );
paintCircularLite( _phylogeny,
getStartingAngle(),
x_pos + radius_ov,
y_pos + radius_ov,
( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
.getWidth() ) ) ),
g );
g.setTransform( _at );
paintOvRectangle( g );
}
}
}
final private void paintPhylogenyLite( final Graphics2D g ) {
//System.out.println( getVisibleRect().x + " " + getVisibleRect().y );
_phylogeny
.getRoot()
.setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
.getWidth() ) ) ) );
_phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
final PhylogenyNodeIterator it;
for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
paintNodeLite( g, it.next() );
}
paintOvRectangle( g );
}
/**
* Paint the root branch. (Differs from others because it will always be a
* single horizontal line).
* @param to_graphics_file
*
* @return new x1 value
*/
final private void paintRootBranch( final Graphics2D g,
final float x1,
final float y1,
final PhylogenyNode root,
final boolean to_pdf,
final boolean to_graphics_file ) {
assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
float d = getXdistance();
if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
}
if ( d < MIN_ROOT_LENGTH ) {
d = MIN_ROOT_LENGTH;
}
if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
}
else {
final double w = PhylogenyMethods.getBranchWidthValue( root );
drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
}
paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
}
final private void paintScale( final Graphics2D g,
int x1,
int y1,
final boolean to_pdf,
final boolean to_graphics_file ) {
x1 += MOVE;
final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
y1 -= 12;
final int y2 = y1 - 8;
final int y3 = y1 - 4;
g.setFont( getTreeFontSet().getSmallFont() );
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else {
g.setColor( getTreeColorSet().getBranchLengthColor() );
}
drawLine( x1, y1, x1, y2, g );
drawLine( x2, y1, x2, y2, g );
drawLine( x1, y3, x2, y3, g );
if ( getScaleLabel() != null ) {
g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
}
}
final private int paintTaxonomy( final Graphics2D g,
final PhylogenyNode node,
final boolean is_in_found_nodes,
final boolean to_pdf,
final boolean to_graphics_file ) {
final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
g.setFont( getTreeFontSet().getLargeItalicFont() );
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
g.setColor( getTreeColorSet().getFoundColor() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
g.setColor( getTreeColorSet().getTaxonomyColor() );
}
final double start_x = node.getXcoord() + 3 + TreePanel.HALF_BOX_SIZE;
final double start_y = node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
_sb.setLength( 0 );
if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
_sb.append( taxonomy.getTaxonomyCode() );
_sb.append( " " );
}
if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
&& !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
_sb.append( taxonomy.getScientificName() );
_sb.append( " (" );
_sb.append( taxonomy.getCommonName() );
_sb.append( ") " );
}
else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
_sb.append( taxonomy.getScientificName() );
_sb.append( " " );
}
else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
_sb.append( taxonomy.getCommonName() );
_sb.append( " " );
}
}
else if ( _control_panel.isShowTaxonomyScientificNames() ) {
if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
_sb.append( taxonomy.getScientificName() );
_sb.append( " " );
}
}
else if ( _control_panel.isShowTaxonomyCommonNames() ) {
if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
_sb.append( taxonomy.getCommonName() );
_sb.append( " " );
}
}
final String label = _sb.toString();
/* GUILHEM_BEG */
if ( ( label.length() > 0 ) && ( node.getNodeData().isHasSequence() )
&& node.getNodeData().getSequence().equals( _query_sequence ) ) {
// invert font color and background color to show that this is the query sequence
final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
false,
false ) )
.getBounds();
g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
g.setColor( getTreeColorSet().getBackgroundColor() );
}
/* GUILHEM_END */
TreePanel.drawString( label, start_x, start_y, g );
if ( is_in_found_nodes ) {
return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
}
else {
return getTreeFontSet()._fm_large_italic.stringWidth( label );
}
}
final private void paintUnrooted( final PhylogenyNode n,
final double low_angle,
final double high_angle,
final boolean radial_labels,
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file ) {
if ( n.isRoot() ) {
n.setXcoord( getWidth() / 2 );
n.setYcoord( getHeight() / 2 );
paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
}
if ( n.isExternal() ) {
paintNodeDataUnrootedCirc( g,
n,
to_pdf,
to_graphics_file,
radial_labels,
( high_angle + low_angle ) / 2,
isInFoundNodes( n ) );
return;
}
final float num_enclosed = n.getNumberOfExternalNodes();
final float x = n.getXcoord();
final float y = n.getYcoord();
double current_angle = low_angle;
// final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
// final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
// final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
// final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
final PhylogenyNode desc = n.getChildNode( i );
/// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
// || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
// || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
// || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
// continue;
// }
//if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
// continue;
//}
//if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
// continue;
// }
final int desc_num_enclosed = desc.getNumberOfExternalNodes();
final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
float length;
if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
if ( desc.getDistanceToParent() < 0 ) {
length = 0;
}
else {
length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
}
}
else {
length = getUrtFactor();
}
final double mid_angle = current_angle + arc_size / 2;
final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
desc.setXcoord( new_x );
desc.setYcoord( new_y );
paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
current_angle += arc_size;
assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
drawLine( x, y, new_x, new_y, g );
}
}
final private void paintUnrootedLite( final PhylogenyNode n,
final double low_angle,
final double high_angle,
final Graphics2D g,
final float urt_ov_factor ) {
if ( n.isRoot() ) {
final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / 2 );
final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / 2 );
n.setXSecondary( x_pos );
n.setYSecondary( y_pos );
}
if ( n.isExternal() ) {
return;
}
final float num_enclosed = n.getNumberOfExternalNodes();
final float x = n.getXSecondary();
final float y = n.getYSecondary();
double current_angle = low_angle;
for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
final PhylogenyNode desc = n.getChildNode( i );
final int desc_num_enclosed = desc.getNumberOfExternalNodes();
final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
float length;
if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
if ( desc.getDistanceToParent() < 0 ) {
length = 0;
}
else {
length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
}
}
else {
length = urt_ov_factor;
}
final double mid_angle = current_angle + arc_size / 2;
final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
desc.setXSecondary( new_x );
desc.setYSecondary( new_y );
if ( isInFoundNodes( desc ) ) {
g.setColor( getTreeColorSet().getFoundColor() );
drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
g.setColor( getTreeColorSet().getOvColor() );
}
paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
current_angle += arc_size;
drawLine( x, y, new_x, new_y, g );
}
}
final private void pasteSubtree( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
JOptionPane.showMessageDialog( this,
"No tree in buffer (need to copy or cut a subtree first)",
"Attempt to paste with empty buffer",
JOptionPane.ERROR_MESSAGE );
return;
}
final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
final Object[] options = { "As sibling", "As descendant", "Cancel" };
final int r = JOptionPane.showOptionDialog( this,
"How to paste subtree" + label + "?",
"Paste Subtree",
JOptionPane.CLOSED_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
options,
options[ 2 ] );
boolean paste_as_sibling = true;
if ( r == 1 ) {
paste_as_sibling = false;
}
else if ( r != 0 ) {
return;
}
final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
buffer_phy.setAllNodesToNotCollapse();
buffer_phy.preOrderReId();
if ( paste_as_sibling ) {
if ( node.isRoot() ) {
JOptionPane.showMessageDialog( this,
"Cannot paste sibling to root",
"Attempt to paste sibling to root",
JOptionPane.ERROR_MESSAGE );
return;
}
buffer_phy.addAsSibling( node );
}
else {
buffer_phy.addAsChild( node );
}
if ( getCopiedAndPastedNodes() == null ) {
setCopiedAndPastedNodes( new HashSet<PhylogenyNode>() );
}
getCopiedAndPastedNodes().addAll( PhylogenyMethods.obtainAllNodesAsSet( buffer_phy ) );
_phylogeny.externalNodesHaveChanged();
_phylogeny.hashIDs();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
repaint();
}
final public int print( final Graphics g, final PageFormat page_format, final int page_index )
throws PrinterException {
if ( page_index > 0 ) {
return ( NO_SUCH_PAGE );
}
else {
final Graphics2D g2d = ( Graphics2D ) g;
g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
// Turn off double buffering !?
paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
// Turn double buffering back on !?
return ( PAGE_EXISTS );
}
}
final void recalculateMaxDistanceToRoot() {
_max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
}
/**
* Remove all edit-node frames
*/
final void removeAllEditNodeJFrames() {
for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
if ( _node_frames[ i ] != null ) {
_node_frames[ i ].dispose();
_node_frames[ i ] = null;
}
}
_node_frame_index = 0;
}
/**
* Remove a node-edit frame.
*/
final void removeEditNodeFrame( final int i ) {
_node_frame_index--;
_node_frames[ i ] = null;
if ( i < _node_frame_index ) {
for( int j = 0; j < _node_frame_index - 1; j++ ) {
_node_frames[ j ] = _node_frames[ j + 1 ];
}
_node_frames[ _node_frame_index ] = null;
}
}
final void reRoot( final PhylogenyNode node ) {
if ( !getPhylogeny().isRerootable() ) {
JOptionPane.showMessageDialog( this,
"This is not rerootable",
"Not rerootable",
JOptionPane.WARNING_MESSAGE );
return;
}
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
JOptionPane.showMessageDialog( this,
"Cannot reroot in unrooted display type",
"Attempt to reroot tree in unrooted display",
JOptionPane.WARNING_MESSAGE );
return;
}
getPhylogeny().reRoot( node );
getPhylogeny().recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
resetPreferredSize();
getMainPanel().adjustJScrollPane();
repaint();
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
getControlPanel().showWhole();
}
}
final void resetNodeIdToDistToLeafMap() {
_nodeid_dist_to_leaf = new HashMap<Integer, Short>();
}
//******************************************START CHANGED**********************************************************//
public void resetPreferredSize() {
//void resetPreferredSize() { //changed default -> public
//********************************************END**********************************************************//
if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
return;
}
int x = 0;
int y = 0;
y = TreePanel.MOVE
+ ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
if ( getControlPanel().isDrawPhylogram() ) {
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil
.roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
}
else {
if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil.roundToInt( getXdistance()
* ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
}
else {
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil.roundToInt( getXdistance()
* ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
}
}
setPreferredSize( new Dimension( x, y ) );
}
final void setArrowCursor() {
setCursor( ARROW_CURSOR );
repaint();
}
final void setControlPanel( final ControlPanel atv_control ) {
_control_panel = atv_control;
}
final private void setCopiedAndPastedNodes( final Set<PhylogenyNode> copied_and_pasted_nodes ) {
getMainPanel().setCopiedAndPastedNodes( copied_and_pasted_nodes );
}
final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
}
final void setEdited( final boolean edited ) {
_edited = edited;
}
final void setFoundNodes( final Set<PhylogenyNode> found_nodes ) {
_found_nodes = found_nodes;
}
final private void setInOv( final boolean in_ov ) {
_in_ov = in_ov;
}
final void setInOvRect( final boolean in_ov_rect ) {
_in_ov_rect = in_ov_rect;
}
final void setLargeFonts() {
getTreeFontSet().largeFonts();
}
final void setLastMouseDragPointX( final float x ) {
_last_drag_point_x = x;
}
final void setLastMouseDragPointY( final float y ) {
_last_drag_point_y = y;
}
final void setLongestExtNodeInfo( final int i ) {
_longest_ext_node_info = i;
}
final void setMediumFonts() {
getTreeFontSet().mediumFonts();
}
final private void setOvMaxHeight( final float ov_max_height ) {
_ov_max_height = ov_max_height;
}
final private void setOvMaxWidth( final float ov_max_width ) {
_ov_max_width = ov_max_width;
}
final void setOvOn( final boolean ov_on ) {
_ov_on = ov_on;
}
final private void setOvXcorrectionFactor( final float f ) {
_ov_x_correction_factor = f;
}
final private void setOvXDistance( final float ov_x_distance ) {
_ov_x_distance = ov_x_distance;
}
final private void setOvXPosition( final int ov_x_position ) {
_ov_x_position = ov_x_position;
}
final private void setOvYDistance( final float ov_y_distance ) {
_ov_y_distance = ov_y_distance;
}
final private void setOvYPosition( final int ov_y_position ) {
_ov_y_position = ov_y_position;
}
final private void setOvYStart( final int ov_y_start ) {
_ov_y_start = ov_y_start;
}
/**
* Set parameters for printing the displayed tree
*
* @param x
* @param y
*/
//******************************************START CHANGED**********************************************************//
public void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
// void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) { default -> public - changed
//********************************************END**********************************************************//
// updateStyle(); not needed?
if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
initNodeData();
if ( recalc_longest_ext_node_info ) {
calculateLongestExtNodeInfo();
}
int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
if ( ext_nodes == 1 ) {
ext_nodes = max_depth;
if ( ext_nodes < 1 ) {
ext_nodes = 1;
}
}
updateOvSizes();
float xdist = 0;
float ov_xdist = 0;
if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
}
else {
xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
}
float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
if ( xdist < 0.0 ) {
xdist = 0.0f;
}
if ( ov_xdist < 0.0 ) {
ov_xdist = 0.0f;
}
if ( ydist < 0.0 ) {
ydist = 0.0f;
}
setXdistance( xdist );
setYdistance( ydist );
setOvXDistance( ov_xdist );
final double height = _phylogeny.getHeight();
if ( height > 0 ) {
final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
setXcorrectionFactor( corr > 0 ? corr : 0 );
final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
}
else {
setXcorrectionFactor( 0 );
setOvXcorrectionFactor( 0 );
}
_circ_max_depth = max_depth;
setUpUrtFactor();
}
}
final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
_graphics_type = graphics_type;
setTextAntialias();
}
final private void setScaleDistance( final double scale_distance ) {
_scale_distance = scale_distance;
}
final private void setScaleLabel( final String scale_label ) {
_scale_label = scale_label;
}
final void setSmallFonts() {
getTreeFontSet().smallFonts();
}
final void setStartingAngle( final double starting_angle ) {
_urt_starting_angle = starting_angle;
}
final void setSuperTinyFonts() {
getTreeFontSet().superTinyFonts();
}
final void setTextAntialias() {
if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
_rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
}
else {
_rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
}
}
if ( getMainPanel().getOptions().isAntialiasScreen() ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) {
_rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
}
else {
_rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
}
try {
_rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
}
catch ( final Throwable e ) {
_rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
}
}
else {
_rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
_rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
}
}
final void setTinyFonts() {
getTreeFontSet().tinyFonts();
}
/**
* Set a phylogeny tree.
*
* @param t
* an instance of a Phylogeny
*/
final void setTree( final Phylogeny t ) {
_phylogeny = t;
}
final void setTreeFile( final File treefile ) {
_treefile = treefile;
}
final private void setUpUrtFactor() {
final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
: getVisibleRect().height;
if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
}
else {
final int max_depth = _circ_max_depth;
if ( max_depth > 0 ) {
setUrtFactor( d / ( 2 * max_depth ) );
}
else {
setUrtFactor( d / 2 );
}
}
setUrtFactorOv( getUrtFactor() );
}
final private void setUrtFactor( final float urt_factor ) {
_urt_factor = urt_factor;
}
final private void setUrtFactorOv( final float urt_factor_ov ) {
_urt_factor_ov = urt_factor_ov;
}
final void setWaitCursor() {
setCursor( WAIT_CURSOR );
repaint();
}
final void setXcorrectionFactor( final float f ) {
_x_correction_factor = f;
}
final void setXdistance( final float x ) {
_x_distance = x;
}
final void setYdistance( final float y ) {
_y_distance = y;
}
final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
try {
if ( ( node.getNodeName().length() > 0 )
|| ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
|| ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
|| ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
|| node.getBranchData().isHasConfidences() ) {
_popup_buffer.setLength( 0 );
short lines = 0;
if ( node.getNodeName().length() > 0 ) {
lines++;
_popup_buffer.append( node.getNodeName() );
}
if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
lines++;
boolean enc_data = false;
final Taxonomy tax = node.getNodeData().getTaxonomy();
if ( _popup_buffer.length() > 0 ) {
_popup_buffer.append( "\n" );
}
if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
_popup_buffer.append( "[" );
_popup_buffer.append( tax.getTaxonomyCode() );
_popup_buffer.append( "]" );
enc_data = true;
}
if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
if ( enc_data ) {
_popup_buffer.append( " " );
}
_popup_buffer.append( tax.getScientificName() );
enc_data = true;
}
if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
if ( enc_data ) {
_popup_buffer.append( " (" );
}
else {
_popup_buffer.append( "(" );
}
_popup_buffer.append( tax.getCommonName() );
_popup_buffer.append( ")" );
enc_data = true;
}
if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
if ( enc_data ) {
_popup_buffer.append( " (" );
}
else {
_popup_buffer.append( "(" );
}
_popup_buffer.append( tax.getAuthority() );
_popup_buffer.append( ")" );
enc_data = true;
}
if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
if ( enc_data ) {
_popup_buffer.append( " [" );
}
else {
_popup_buffer.append( "[" );
}
_popup_buffer.append( tax.getRank() );
_popup_buffer.append( "]" );
enc_data = true;
}
if ( tax.getSynonyms().size() > 0 ) {
if ( enc_data ) {
_popup_buffer.append( " " );
}
_popup_buffer.append( "[" );
int counter = 1;
for( final String syn : tax.getSynonyms() ) {
if ( !ForesterUtil.isEmpty( syn ) ) {
enc_data = true;
_popup_buffer.append( syn );
if ( counter < tax.getSynonyms().size() ) {
_popup_buffer.append( ", " );
}
}
counter++;
}
_popup_buffer.append( "]" );
}
if ( !enc_data ) {
if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
_popup_buffer.append( "[" );
_popup_buffer.append( tax.getIdentifier().getProvider() );
_popup_buffer.append( "] " );
}
_popup_buffer.append( tax.getIdentifier().getValue() );
}
}
}
if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
lines++;
boolean enc_data = false;
if ( _popup_buffer.length() > 0 ) {
_popup_buffer.append( "\n" );
}
final Sequence seq = node.getNodeData().getSequence();
if ( seq.getAccession() != null ) {
_popup_buffer.append( "[" );
if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
_popup_buffer.append( seq.getAccession().getSource() );
_popup_buffer.append( "=" );
}
_popup_buffer.append( seq.getAccession().getValue() );
_popup_buffer.append( "]" );
enc_data = true;
}
if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
if ( enc_data ) {
_popup_buffer.append( " [" );
}
else {
_popup_buffer.append( "[" );
}
_popup_buffer.append( seq.getSymbol() );
_popup_buffer.append( "]" );
enc_data = true;
}
if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
if ( enc_data ) {
_popup_buffer.append( " " );
}
_popup_buffer.append( seq.getName() );
}
}
if ( node.getNodeData().isHasDate() ) {
lines++;
if ( _popup_buffer.length() > 0 ) {
_popup_buffer.append( "\n" );
}
_popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
}
if ( node.getNodeData().isHasDistribution() ) {
lines++;
if ( _popup_buffer.length() > 0 ) {
_popup_buffer.append( "\n" );
}
_popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
}
if ( node.getBranchData().isHasConfidences() ) {
final List<Confidence> confs = node.getBranchData().getConfidences();
for( final Confidence confidence : confs ) {
lines++;
if ( _popup_buffer.length() > 0 ) {
_popup_buffer.append( "\n" );
}
if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
_popup_buffer.append( "[" );
_popup_buffer.append( confidence.getType() );
_popup_buffer.append( "] " );
}
else {
_popup_buffer.append( "[?] " );
}
_popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil
.round( confidence.getValue(), getOptions()
.getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
}
}
if ( _popup_buffer.length() > 0 ) {
if ( !getConfiguration().isUseNativeUI() ) {
_rollover_popup
.setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
_rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
if ( isInFoundNodes( node ) ) {
_rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
_rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
}
else {
//******************************************START Changed**********************************************************//
// Changed _rollover_popup foreground to red (getDupBoxCol() is red in config
if(AppletParams.isEitherTPorTDForLANLorBHB() || AppletParams.isArchaeopteryxForBHBorLANL()) {
_rollover_popup.setForeground( getTreeColorSet().getDuplicationBoxColor() );
}
else {
_rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
}
//********************************************END**********************************************************//
}
}
else {
_rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
}
_rollover_popup.setText( _popup_buffer.toString() );
_node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
_rollover_popup,
e.getLocationOnScreen().x + 10,
e.getLocationOnScreen().y
- ( lines * 20 ) );
_node_desc_popup.show();
}
}
}
catch ( final Exception ex ) {
// Do nothing.
}
}
final private void showNodeEditFrame( final PhylogenyNode n ) {
if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
// pop up edit box for single node
_node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
_node_frame_index++;
}
else {
JOptionPane.showMessageDialog( this, "too many node windows are open" );
}
}
final private void showNodeFrame( final PhylogenyNode n ) {
if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
// pop up edit box for single node
_node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
_node_frame_index++;
}
else {
JOptionPane.showMessageDialog( this, "too many node windows are open" );
}
}
final void subTree( final PhylogenyNode node ) {
/*if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
JOptionPane.showMessageDialog( this,
"Cannot get a sub/super tree in unrooted display",
"Attempt to get sub/super tree in unrooted display",
JOptionPane.WARNING_MESSAGE );
return;
}
if ( node.isExternal() ) {
JOptionPane.showMessageDialog( this,
"Cannot get a subtree of a external node",
"Attempt to get subtree of external node",
JOptionPane.WARNING_MESSAGE );
return;
}
if ( node.isRoot() && ( _subtree_index < 1 ) ) {
JOptionPane.showMessageDialog( this,
"Cannot get a subtree of the root node",
"Attempt to get subtree of root node",
JOptionPane.WARNING_MESSAGE );
return;
}
if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
_phylogenies[ _subtree_index++ ] = _phylogeny;
_phylogeny = _phylogeny.subTree( node );
updateSubSuperTreeButton();
}
else if ( node.isRoot() && ( _subtree_index >= 1 ) ) {
superTree();
}
_main_panel.getControlPanel().showWhole();
repaint();*/
//******************************************START CHANGED**********************************************************//
if(AppletParams.isEitherTPorTDForAll()){
newWindowSubtree.subTree(node, _phylogeny, subTreePanel);
}
else{
if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
_phylogenies[ _subtree_index++ ] = _phylogeny;
_phylogeny = _phylogeny.subTree( node );
updateSubSuperTreeButton();
}
else if ( node.isRoot() && ( _subtree_index >= 1 ) ) {
superTree();
}
_main_panel.getControlPanel().showWhole();
repaint();
}
// ENTIRE METHOD of subTree(node) has been overwritten - changed
//********************************************END**********************************************************//
}
final void superTree() {
// _phylogenies[ _subtree_index ] = null;
// _phylogeny = _phylogenies[ --_subtree_index ];
// updateSubSuperTreeButton();
//******************************************START CHANGED**********************************************************//
if(AppletParams.isEitherTPorTDForAll()){
newWindowSubtree.superTree();
}
// ENTIRE METHOD of superTree() has been overwritten - changed
else{
_phylogenies[ _subtree_index ] = null;
_phylogeny = _phylogenies[ --_subtree_index ];
updateSubSuperTreeButton();
}
//********************************************END**********************************************************//
}
final void swap( final PhylogenyNode node ) {
if ( !node.isExternal() ) {
_phylogeny.swapChildren( node );
}
repaint();
}
final private void switchDisplaygetPhylogenyGraphicsType() {
switch ( getPhylogenyGraphicsType() ) {
case RECTANGULAR:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
break;
case EURO_STYLE:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
break;
case ROUNDED:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
break;
case CURVED:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
break;
case TRIANGULAR:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
break;
case CONVEX:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
break;
case UNROOTED:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
break;
case CIRCULAR:
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
break;
default:
throw new IllegalStateException( "unkwnown display type: " + getPhylogenyGraphicsType() );
}
if ( getControlPanel().getDynamicallyHideData() != null ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
getControlPanel().getDynamicallyHideData().setEnabled( false );
}
else {
getControlPanel().getDynamicallyHideData().setEnabled( true );
}
}
if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
getControlPanel().setDrawPhylogramEnabled( true );
}
else {
getControlPanel().setDrawPhylogramEnabled( false );
}
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
.setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
}
else {
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
}
}
final void taxColor() {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
}
setWaitCursor();
Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
setArrowCursor();
repaint();
}
final void updateOvSettings() {
switch ( getOptions().getOvPlacement() ) {
case LOWER_LEFT:
setOvXPosition( OV_BORDER );
setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
break;
case LOWER_RIGHT:
setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
break;
case UPPER_RIGHT:
setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
setOvYPosition( OV_BORDER );
setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
break;
default:
setOvXPosition( OV_BORDER );
setOvYPosition( OV_BORDER );
setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
break;
}
}
final void updateOvSizes() {
if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) {
setOvOn( true );
float l = getLongestExtNodeInfo();
final float w_ratio = getOvMaxWidth() / getWidth();
l *= w_ratio;
final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
float ov_xdist = 0;
if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
}
else {
ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
}
float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
if ( ov_xdist < 0.0 ) {
ov_xdist = 0.0f;
}
if ( ydist < 0.0 ) {
ydist = 0.0f;
}
setOvXDistance( ov_xdist );
final double height = _phylogeny.getHeight();
if ( height > 0 ) {
final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
}
else {
setOvXcorrectionFactor( 0 );
}
}
else {
setOvOn( false );
}
}
final void updateSubSuperTreeButton() {
if ( _subtree_index < 1 ) {
getControlPanel().deactivateButtonToReturnToSuperTree();
}
else {
getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
}
}
final void zoomInDomainStructure() {
if ( _domain_structure_width < 2000 ) {
_domain_structure_width *= 1.2;
}
}
final void zoomOutDomainStructure() {
if ( _domain_structure_width > 20 ) {
_domain_structure_width *= 0.8;
}
}
final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
}
final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
}
final private static boolean isSequenceEmpty( final Sequence seq ) {
return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
&& ForesterUtil.isEmpty( seq.getSymbol() );
}
final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
&& ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
.getSynonyms().isEmpty() );
}
final private static boolean plusPressed( final int key_code ) {
return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
|| ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
}
final private class SubtreeColorizationActionListener implements ActionListener {
JColorChooser _chooser;
PhylogenyNode _node;
SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
_chooser = chooser;
_node = node;
}
@Override
public void actionPerformed( final ActionEvent e ) {
final Color c = _chooser.getColor();
if ( c != null ) {
colorizeSubtree( c, _node );
}
}
}
//******************************************START**********************************************************//
public void setPhylogeny(Phylogeny phylogeny){
_phylogeny = phylogeny;
}
public Phylogeny getCurrentPhylogeny(){
return _phylogeny;
}
public static void reset_subtree_index(){
_subtree_index = 0;
}
public static void set_subtree_index(int n){
_subtree_index = n;
}
public static int get_subtree_index(){
return _subtree_index;
}
public void updateSubSuperTreeButton(boolean deactivate) {
if ( deactivate ) {
getControlPanel().deactivateButtonToReturnToSuperTree();
}
else {
getControlPanel().activateButtonToReturnToSuperTree( 0 );
}
}
public File get_tree_file() {
return _treefile;
}
public void set_tree_file(final File treefile) {
_treefile = treefile;
}
public void set_arrow_cursor() {
setCursor(ARROW_CURSOR);
repaint();
}
public PHYLOGENY_GRAPHICS_TYPE get_phylogeny_graphicsType() {
return _graphics_type;
}
//********************************************END**********************************************************//
}